Jackstandqueen

Hey guys, so recently I acquired a 1987 Mazda rx7 Turbo II. I am running a half bridge port, a larger turbo, 1600cc injectors, upgraded fuel pump, etc. so I also would need a standalone ecu. With the car came a Haltech e6x and a flying lead (questionable splicing and all). I have never worked with a Haltech before, never mind one so old, but after some research I decided to work with it. However, one thing I found in my research was an effective installation guide. There were a few different (and very helpful) write ups, but nothing that combined in order to install, wire, and set up to tune from start to finish. So I created this! This is by no means all my own writing, and credit is given to the authors in which I pulled information from at the bottom of this post, along with links as to where I got their information. This is also not a complete guide but should be enough, combined with the use of the Haltech wiring guide and installation manual, to get you going. Every RX7 is different and we are all running different set ups. I hope this is helpful to you and good luck with your build!

Information combined from the following authors:

Haltech Manual and wiring diagrams:
Previous Products | Haltech - Engine Management Systems

Brian D. Cain:
Emailed me install notes, pm me if you would like me to forward it to you!

Eric Moreira:
Installation Notes: Haltech install

Wasmac66:
Halwin Setup (Bottom of page): halwinX, Is there a windows7 version? - Official Haltech Forums

Claudio RX-7:
Setting up Serial Port: E6X/F10X Password Error Fix! - Official Haltech Forums

Wiring Diagrams: %09%09http:/www.rx7club.com/haltech-forum-62/haltech-installation-diagrams-setup-tips-850059/

00madz: Halwin 32bit vs. 64bit Vista - Official Haltech Forums


Alex Carnal (Myself)

Along with other Misc. Authors from posts in rx7club.com, Haltech forums, etc.


Lets Begin!

Tools Required:
-An electronic or analog multimeter
-A 3/8 NPT tap
-A good wrench set. I have a Craftsman 100 piece set and it works great.
-Wire stripper/crimper
-Assorted pliers, wrenches, etc.
-Laptop computer to tune (and read this write up)
-9 pin serial cable or usb-serial adapter.
-Rotary tool, Dremel, etc. is not necessary but you will be useful.

Supplies:
-20 feet of 14 gauge wire.
-Electrical tape and zip ties.
-Heat shrink
-Plastic conduit (optional for clean install. AutoZone has 10” for $5.00)
-Spade connectors, the ones that take an existing wire and let you connect one by placing it in the connector and squishing it together.
-Materials to mount Haltech harness (many ways to do this, with plastic, aluminum, etc. it is your choice.)
-Various nuts, bolts, and washers.
-New water pump gasket and gasket from water pump housing to engine block.
Pre-Installation Preparation:
Many things can be removed to make your install easier, but are not necessary. Fortunately I was installing this in the beginning of my build so many things were not installed yet (FMIC, Radiator, etc.). I also have deleted almost everything from my car (PS, A/C, Cruise, etc.) You may have to remove some of these things in order to get to the connections and make the taps you need to install. Use your own digression. I recommend starting by taking the flying lead and separating and labeling wires to where they go. Label each wire with masking tape what it is and where it’s connecting (i.e. Fuel PUMP-> BAT +) this will really help when laying out the harness to see where everything goes. I went as far as bundling each group of wires, heat shrinking them and labeling each individually and one label at the end for what it was for. This may be overkill, but it really helped to see the big picture and to help routing them to the correct place. After you do this it is basically plug and play.

Removal and Prep
- Remove the intercooler and upper intake manifold/throttle body for flying lead, sensor, and harness installation. Remove any couplers, BOV, etc. above the turbo compressor. If running a front mount this may not be necessary

-You do not need to remove the radiator and front clip but it will make life a whole lot easier.

-Unplug all hoses and connectors going to the TB. If you have the TB mod that simplifies things but now remove the VDI and TB all in one piece.

-Remove the air conditioning components. This is an optional step but is a good time to delete a/c. It also creates more working room and can be reinstalled later.

-During factory ECU removal, there will be one harness going off towards the driver's side of the car. It is remaining intact and will not be removed. The only portion removed is the passenger side, engine wiring harness. Went in doubt, Read the Haltech manual and refer to the wiring diagram in both that and the factory manual.

- The windshield washer motor need to be rewired since the factory engine harness (passenger side) will be removed with the wiper motor's harness bundled in. During the removal of the factory ECU's engine wiring harness, the wiring for this motor will be cut as it goes to a rectangular, orange connector mounted on the inside passenger fender well above the stock ECU. Simply unplug this orange connector when removing the harness, remove the wiper harness bundle, cut the wires, and length to re-splice.

- One additional lead for the factory cockpit's water temperature gauge (C-H gauge) needs to be re-spliced as well as it's bundled on the stock engine wiring harness. It is also going to the same, orange connector clip that contains the wiper harness. It will need to be cut and re-spliced. When running the Haltech's main harness along the firewall, I recommend adding a new wire for this lead if there's intent to retain the factory water temp gauge.

Removing factory EFI and related components
- Remove the Intake and Air flow meter – The AFM will be discarded.
- Remove factory pressure sensor (located near passenger shock tower)
- Remove fuel pump resistor box near passenger headlight and wiring.
- Remove the passenger carpeting and kick panel to remove the factory ECU (Labeled N332, N333, etc.). The Haltech ECU will go in its place.

Air Conditioning set up (S5 only!)

- On the S5 model, the ECU is used as a pass-thru for the A/C compressor. When removing the factory ECU and installing a standalone EFI system, this link gets cut. The end-result is the A/C switch on the dash turns the blower motor on but doesn't engage the A/C compressor itself. Two wires from the 22-pin connector (off of the driver's side harness that did originally plug into the factory ECU) need to be borrowed: Pins 1L (BLUE/WHITE) and 1O (BLUE/ORANGE). The 1L BLUE/WHITE will be spliced into the Haltech PWM output and the 1L BLUE/ORANGE will go to the Haltech's Aux In.
Map settings:
- Haltech Aux Input - AC Request, set to 5V (under Digital Input Functions for E8)
- PWM Output - PWM set to Air Con, Normal Output state, settings to try:
Max TPS A/C 50+%, Max RPM, 4500, Conditions Time Delay 0, Idle time delay 0


Water Temperature Sensor
- The factory water temperature sensor can be retained if it's problematic to remove the water pump housing. The sensor will read approximately 6-7* hotter than actual so all water temperature based corrections maps will work. However, due to the age of the sensor, it is recommended to remove the water pump housing, remove the factory temp sensor, and drill/tap (using 3/4"NPT tap) to use the new Haltech-supplied sensor.

-Unplug the two water sensors just below the thermostat. The lower one is for the AC. It is better to remove this one rather than the top one, which is the water temp sensor. The lower one will be easier to tap.

-In order for a good tap for the sensors you should pull off the water pump housing. Pulling off the water pump housing should be pretty easy and the intake elbow is cake. I tried the 4 10mm bolts but for the life of me it would not come off so I had to do it the hard way, which is described below.

-First try hitting the pullies with a rubber hammer when the 4 bolts are out and they should drop off.
Removing Housing

-If your last resort is to pull the housing because the main pulley didn't come off then read on. To remove the housing you will notice that there are 4 nuts to unscrew and 3 bolts. The bolts are what hold the water pump to the housing and the nuts hold the housing onto the engine block. To remove the studs take a big vice grip with some rubber pieces over the jaws, I used bicycle tires. CAUTION: DOING THIS MAY RUIN THE STUDS AND YOU WILL HAVE TO BUY NEW ONES. With the studs removed you can take the water pump housing off, you just have to remove the BAC hose and some other hose near the bottom of the housing. When re-installing the water pump and housing, use your rotary tool with a sandpaper bit to sand off the old gasket. This makes for a very smooth fitting for the new gasket.


Mounting the Haltech ECU Unit and Fuse block/relays

-I prefer to mount the Haltech ECU in the same location as the stock ECU. Position the ECU with its wiring harness connection facing the passenger side for ease of harness installation.

- Fuse block and relay mounting: You can mount the fuse block and relays a number of ways. One way (Brian’s method) is to mount the two relays and fuse block in the location of the factory cruise control box on the passenger side fender behind the strut tower. Removal of the cruise control is necessary for this.
Another way is Eric’s method:

“I made a plate for my Haltech and Greddy unit to attach onto. I used 1/4" stiff plastic. I happen to have some in my basement which is white and very stiff. I measured out an 8" by 10" area and then cut it with my Sears rotary tool.
At the top of the 8" side there needs to be two holes 4 1/4" apart. I placed the first one 1" in from the side and 1/2" down from the top. This way it will fit where the top two screws for the condenser used to go.”

The way I mounted them was I went and bought aluminum at the hardware store and made a mounting plate to be mounted in the stock ECU location. I mounted the fuse block and relays to the left (not harness connection side) of the ECU on this plate. I then made an aluminum cover that bolts onto the plate over the ecu/fuse/relays. This way it is all easy to access (four bolts) and all wiring is hidden. It is also protected from being kicked by your passenger.


Main Wiring Loom/Flying Leads/Fuses/Relays

- Many of the leads on the Haltech harness will not be used (approximately 1/3rd to 1/2).

- Run the Haltech harness through the firewall hole where the factory engine wiring harness was run.

- Mount the fuse block and main relays. An example can be seen here:

- The Fuse Block contains three blade fuses: 3A ECU, 10A Fuel Injectors +12VDC, and 20A Fuel Pump +12VDC. The Haltech uses its own relays and fuse bank for the ECU, Fuel Pump, and Injectors. The Fuel Pump is primed directly by the Haltech.

- The two relays used are for Fuel Pump (contains the two 12AWG ORANGE leads) and the ECU/Injectors.

- The relays' +12VDC switching lead can be wire either to the main ignition relay or to the 6-prong, green connector clip (top middle lead)

- When the main wiring harness is run across the firewall during the portion of the installation where injectors and sensors are being wired up, the three 12AWG flying leads need to be sent directly to the battery:
BLACK (Gnd) to – post
RED (ECU/Injector Const +12VDC) to + post
ORANGE (Fuel Pump Const +12VDC) to + post

Providing Switched Power for Haltech Relays

- The GREEN and GRAY relay switching leads may be combined together into one lead as they drawl minimal current.

- 6-lead plug near the driver's side; all female; white (AAS harness): The bottom center (black or blue w/ red stripe)
OR
- On the main ignition harness near the main ignition relay (near the trailing igniter pack), there is a 2-lead white connector plug. The thin-gaged (18AWG) black with white striped and red notched lead can be spliced into.

Fuel Pump Wiring

-Pop the hatch and pull up the carpeting and sound damping so you can access the fuel pump. You will also need to pull back the side flashing so you can wire the fuel pump.

-Take out the rear carpeting along with the storage bins (Optional). To do this you just pull the carpet up as much as you can and then unscrew the snaps using a Phillips screwdriver. Once you have those out you will see 5 bolts going down the middle of the storage holes. Take those out. Also take out the 5 bolts that hold the fiberglass to the frame behind the back seats. Now you can rewire the fuel pump

-After wiring the three main 12AWG flying leads to the battery, there will be a second 12AWG ORANGE lead leftover. This lead needs to be sent to the back of the car to the Fuel Pump (BLACK/WHITE on 4-lead pump wiring harness). I also recommend at this time wiring the BLACK lead on the Fuel Pump harness directly to a chassis ground spot nearby. The two remaining RED and BLUE leads on the Fuel Pump Harness are used for fuel level sending unit.

O2 Sensor
- The use of a heated O2 sensor is acceptable but not required. The use of any narrowband O2 sensor is recommended for Closed O2 Loop control. If using a heated sensor, use a BLACK (Gnd) and RED/GRAY (switched +12VDC) off of the Haltech harness for sensor ground and power.
Intake Air Temp and Coolant Temp Sensors
The Haltech requires use of GM Intake air and coolant temp sensors. The flying lead comes with these replacement sensors, however if you do not have them, see the parts list at the beginning of this write up.

-In order for a good tap for the sensors you should pull off the intake pipe that has the air sensor in it.

- The factory air temp sensor will need to be replaced with the GM. It can be placed anywhere prior to the throttle body, preferably in the inlet adaptor that bolts to the throttle body. If using an aftermarket inlet (FMIC setup, etc.) many inlets have a hole tapped. It will need to be a 3/4"NPT tap. Use of thread sealant or Teflon is recommended.

Wiring:

- The Air Temperature sensor GRAY and BLACK (Gnd) and can be wired to either wire of grey connector clip.
- Water Temperature sensor PURPLE and BLACK (Gnd) and can be wired to either wire of black connector clip.

Throttle Position Sensor (TPS)

- If using a Series 4 86-88 FC3S, you must either use the Haltech-supplied TPS or install a series 5 TPS setup. Refer to wiring diagram for connector plug hookup. A bracket must be created to mount the TPS to the throttle's primary shaft. The bracket must be strong and solidly mounted to the throttle body while still allowing the shaft to rotate within the TPS. Use of epoxy on the shaft where it goes through the TPS is recommended.
- If this Haltech is being installed on a Series 5 89-91 FC3S or if the throttle body being used on the vehicle is from this same series, then the factory (full-range) TPS may be retained.
- The factory Series 5 throttle body uses two black TPS's with a 6-prong white plug:

TPS side of plug Mazda wiring harness side of plug Haltech 3-lead TPS wiring harness
BLUE BROWN/BLACK/BLUE BLACK (TPS Ground)
PINK BROWN/WHITE ORANGE (5VDC +ve)
YELLOW BLUE/GREEN/RED WHITE (Signal)
ORANGE BROWN/WHITE/BLACK Unused
GREEN/RED GREEN/RED/RED Unused
BLACK/ORANGE BROWN/BLUE/BLUE Unused

MAP Sensor
- The mounting location of the GM 3Bar MAP sensor can be done in many places. I prefer on the fire wall near the wiper motor. The vacuum line source running to the MAP sensor needs to be plumbed to the bottom of the three nipples on the front side of the upper intake manifold. This source is located in the surge plenum of the intake manifold and will yield the smoothest signal to the sensor.

Fuel Injectors
To install the two injectors was very easy. CAUTION: GAS IS EXTREMELY FLAMMABLE SO BE CAREFUL! When you pull out the injectors, be sure to have some towels underneath to catch the gas that WILL SPILL OUT.
- One injector driver per injector: injectors are run on their own individual injector driver
- One power lead from Haltech harness (labeled +13.8VDC INJ on wiring diagram, 13AWG RED) parsed off once for each fuel injector clip for power (some Haltech harnesses already have this done)
- Depending upon injector, the use of the Mazda factory injector clips may be necessary.
- Injectors are always powered with +12VDC; injector leads from Haltech are pulsed ground:
INJ1 Light Blue (Injector 1, Front Primary)
INJ2 Blue with Red Stripe (Injector 2, Rear Primary)
INJ3 Green w/ Red Stripe (Injector 3, Front Secondary)
INJ4 Pink (Injector 4, Rear Secondary)

Crank Angle Sensor
-Route the Trigger plug (the one with 6 wires and 4 of them are shielded with a gray cover) to the CAS. I highly recommend not using the factory Crank Angle Sensor (CAS) white connector clip and instead using the 5-lead white connector clip provided in the Haltech connector kit. Now cut the CAS female end off of the main wiring loom in order to splice it together with the Trigger input.
- There are four wires that come out of the Crank Angle Sensor: RED, WHITE, GREEN, and WHITE/BLACK
- The Haltech trigger harness is shielded and contains these small-gauge leads: BLUE, RED, GREEN, and YELLOW.
- If using an MSD 8509 signal stabilizer as an external reluctor (not recommended) see third wire column.
- Wiring connection:
Mazda CAS Haltech Shielded Trigger Harness (MSD8509)
RED YELLOW Purple
WHITE RED Green
GREEN GREEN Purple
WHITE/BLACK BLUE Green

- When wiring this harness, I highly recommend using a ferrite choke around the trigger harness as well as locating this harness away from the alternator harness to help reduce noise. If there is RF noise on the harness, random 16000rpm spikes will occur.
-In order for the timing to work you must take out the crank angle sensor and point the top at the two cover screws as The HITman states. All you do is take off the cap, unscrew the 2 big screws by the multi tooth wheel, unscrew the bolt on the power steering side of the crank angle sensor and then pull upward. It will pop out so pull carefully. Now you can place it in as close as you can so it is pointing toward the two cap holes and then you can adjust it by twisting the crank angle sensor top when it is in. It sounds confusing but it is very easy.

Factory Igniters and Coils (Providing Switched, Fused +12VDC Power)
- Switched, fused +12VDC power for this hardware is already enabled in the factory power harness. There is no need to remove. On both igniter/coil packs, there are TAN leads that are sent to the 30A EGI main fuse. These TAN leads can be retained with the factory connector clips to keep power using the factory harness. Otherwise, power can be wired up standalone by using a 30A standard automotive relay, fused to at least 20A, with 3 (or 4) individual power leads sent to these TAN leads on the factory hardware.

Ignition
The trailing igniter is easiest to access if you unscrew it and lift it out. With it lifted up you will see a four wire plug with the Pink and White wires along with two others. The other two are for power so leave them alone. Now wire together as described below and remember that they have to ONLY go to the Haltech.
Even though the Haltech E6K and E6X do not natively support it, the use of full sequential ignition on the 2-rotor 13B for simulated direct fire spark is possible by using two factory 2nd gen trailing igniter/coil packs. This is highly preferred over the use of the factory waste-spark setup on the leading plugs. Below are the two ways to install it this way.

Factory Igniters and Coils (Factory Waste Spark Setup, not recommended)
- For use with factory leading igniter w/ dual post coil and factory trailing igniter/coil pack
- Wiring information:
Leading igniter PINK LIGHT GREEN (IGN OUT) on Haltech Harness
Trailing igniter PINK WHITE/BLACK (DIG OUT) on Haltech Harness
Trailing igniter WHITE GREEN/BLACK (AUXOUT +5VDC) on Haltech Harness

- I recommend making all wiring splices prior to the connector clips for ease of ignition component changes.

Factory Igniters and Coils (Sequential Spark Setup, Preferred)
- For use with two pair of factory trailing igniter/coil packs to provide sequential ignition on both trailing and leading plugs (Preferred)
- Since this is more of a custom setup, a more detailed explanation is needed. The factory ignition system uses a dual-post coil w/ dumb igniter for the two leading plugs firing in "waste spark" (one spark is necessary in one chamber; the adjacent chamber gets a wasted spark). It also uses a dumb igniter with a toggle lead for the trailing plugs using two separate coils. This igniter receives a toggle lead (5VDC) that acts as a switch to tell the igniter which coil to fire (either front trailing or rear trailing). To use this same sequential spark for the two leading plugs, an additional trailing igniter coil/pack can be used by duplicating this same methodology. In this case, the leading igniter/dual post coil pack is entirely removed and replaced with this additional trailing igniter/coil pack. Due to space constraints in the chassis, some modification to the igniter and coils (in terms of mounting) may be needed.
- Wiring information (assuming the use of two trailing-type igniters and four coils):

Leading igniter PINK LIGHT GREEN (IGN OUT) on Haltech Harness
Leading igniter WHITE GREEN/BLACK (Auxout +5VDC) on Haltech Harness
Trailing igniter PINK WHITE/BLACK (DIG OUT) on Haltech Harness
Trailing igniter WHITE GREEN/BLACK (Auxout +5VDC) on Haltech Harness

- The AUXOUT +5VDC "toggle" lead is sent to both igniters. Using this setup results in simulated Direct Fire ignition, which is highly preferred for any high-powered, boosted setups.
- The remaining leads on the leading igniter are unused but the two TAN leads. These will need to be manually wired up to either the factory EGI harness (spliced into the old connector) or wired in to a dedicated fuse and relay.
This completes the wiring portion of this install!
Now that everything is wired triple check that everything is plugged in and put the car back together enough to run it. You don't need the hood or anything. If you are confident that everything is plugged in you can plug the main loom into the Haltech. Now turn the key to the on position and make sure you hear the fuel pump prime. It is an electrical humming noise that occurs for about 2 or 3 seconds.
Setting up your computer
-The last thing you need is a laptop. If you have/can get one with a 9 pin serial port this will simplify things, however one without will work. I am using a Compaq running Windows 7, but all you need is pretty much ANY notebook with a usb port, a serial to usb adapter, and the correct software. I highly recommend the Keyspan usb-serial adapter.
- Make sure if you are using an adapter you download the correct driver for it to work with your computer.
-If you have the Haltech disk all you need to do is copy all of the contents of the disk onto your C: drive, drag and drop works fine, and then run the program. If not, follow the procedure below.

The easiest way to make this work is to follow these steps:
(This is what I've done to get Haltech run in my Windows 7 64-bit)

-Download the Haltech (Halwin) software here:

http://www.haltech.com/wp-content/up...lwinx_1.26.zip

-Download this file and unzip it into the same folder as you put the unzipped Halwin setup files:
http://toastytech.com/files/Is3Engine.zip

-In the Halwin installation file folder, you should see "setup.exe" file, right click, click "Properties"

-In "General" tab, click "Unblock".

-In "Compatibility" tab, tick "Run this program as administrator".

-Repeat the step 2~4 for the file "_ISDEL.EXE" in the same folder.

-Run the setup32.exe as administrator (not sure if it's ok if not running as admin). You should be able to install Halwin 1.26.

-After install, follow this link to configure you USB simulated COM port:
E6X/F10X Password Error Fix! - Official Haltech Forums

Then you are good to go!


If when you boot up Haltech and try to go Online it just sits there, you have a com port problem. Search the forums for solutions to these, lots of good write ups.


Haltech Ignition Setup Page
- These settings apply to both the Waste Spark setup and the Sequential Spark setups.
Trigger Input INTERNAL RELUCTOR
Trigger Gain 1
Home Input INTERNAL RELUCTOR
Home Gain 2
Trigger Mode ADAPTIVE
Trigger Angle 65*BTDC (use this figure to start with even though it will be adjusted later on)

Trigger Type MULTITOOTH
Number of Teeth 24
Tooth Offset 11 (for Stock CAS insertion) or 3 (for HITman method)

Spark Mode DISTRIBUTOR
Engine Type ROTARY
Output Type CONSTANT CHARGE (not Constant Duty; stock igniters are 'dumb' type)
Coil Charge Time 4.8ms
Output Edge FALLING (If using an E6X, double-check this setting in Halwin_X to ensure it is not set to RISING)

Inserting/Stabbing Mazda CAS
- This step must be done all wiring is complete, all sensors verified, with the engine already running on a base map.
- If the Crank Angle Sensor has never been removed, then disregard this step.
- If using an aftermarket pulley, any timing mark can be used for Lock Timing degrees as long as the timing mark is known-good.
- Stock Method (preferred): Manually rotate engine to 5*ATDC (Yellow Marker aligned with timing mark on front cover). With the CAS's black cap removed, insert the CAS with the two pickup points pointing towards 2:30 o'clock and 8:30 o'clock.
The gear on the bottom of the CAS will be aligned to the notch on the CAS's aluminum body properly.
- HITman's method: Manually rotate engine where 5ATDC yellow marker on pulley lines w/ timing marker on front cover. With the CAS's black cap removed, insert with both pickup points approximately lined up w/ CAS's cap's screw holes.
- Top Dead Centre (and approximately 5*ATDC) can be found by positioning the crankshaft's front key indexer to 9'oclock.


Now you should be good to start dialing in the Car! This is by no means a complete guide to this install but should cover all the basics. If there is any information to add/incorrect please give your input. Good Luck!! Brap Brap

unek87

I used Brian's notes for my e6k over the last few years . I had to search for it though . So it cool you got it back up on here . I talk to him a few months ago through email . Said he would send me a better base map once I'm
Ready , which should be in the next week or so hopefully .

dvs-knight

quick question i have a e6k i want to install in my s5 turboll i wanted to know if its mandatory to use the haltech fusebox because i was planing to wire the ecu in like a piggyback system

ACR_RX-7

iTrader: (1)

It is mandatory to use the Haltech Fuse box, since it powers the Haltech ECU, the Injectors, and the fuel pump. All of these are controlled by the Haltech.

The haltech is a full function standalone, why would you want to run it as a piggy-back?

Do it right and wire it in as the only controller.

gxl90rx7

iTrader: (1)

i didnt use the haltech relays because all the relays you need are already factory installed.. way cleaner install. my ps1k FD installation uses all the factory relays, including engine and fan and fuel pump resistor relay no problems. i would not call that a piggyback at all

you definitely want to replace the engine harness with the new haltech harness, most 20+ year old harnesses are junk

ACR_RX-7

iTrader: (1)

[QUOTE=gxl90rx7;12103026]i didnt use the haltech relays because all the relays you need are already factory installed.. way cleaner install. my ps1k FD installation uses all the factory relays, including engine and fan and fuel pump resistor relay no problems. i would not call that a piggyback at all
[quote]

I should have rephrased.

Mandatory, no. IMO I would use fresh, new relays, not the 20+ year old FC relays.
I personally like to separate the new engine controller from the old wiring completely.



Absolutely yes. You may not see it, but there are often micro cracks in the insulation in the middle of a harness bundle. Micro breaks cause huge issues.