Im looking into MS, but Im still in the dark on a few things. Before I get flamed for it, I have spent the last hour searching for these few questions and havent found much.

Will I be able to leave the chassis (drivers-side) harness plugged into the stock ecu port? (for interior lights and controls)

What is this 2nd VR thing and what will I have to do about it? (has to do with the CAS I believe)

 

I cannot answer your first question but I can answer the second.

Basically the CAS has two Variable Reluctance sensors instead of one. Depending on whether or not you follow the "Aaron cake Megasquirt" guide or something else. There are a couple ways to approach it. The first, and more straight forward is to buy the individual components and build the circuit in the prototype area on the v3 board.
The other option is to purchase the zeal daughterboard via DIYAutoTune (best Megasquirt purchasing site!) which has the circuit pre-built and wire that to the main board via a few wires for input and output.

 

S5 TII guy here as well.

First question: The ECU on S5 TII cars (or any FC for that matter) doesn't control any of those things. So you should be getting rid of the ecu, if you look at the writeup by aaroncake, he shows you exactly how to keep the stuff that the megasquirt harness doesn't replace (windshield wipers and temp gauge)

http://www.aaroncake.net/rx-7/megasq...tockWiring.asp

With his writeup I ran into a bit of an issue, my S5 N/A convertible's wiring had the alternator wiring on the body harness, not in the engine harness like his writeup says. So pay attention here, the plug in the back of the alternator is kind of unique so it's not hard to miss.


Second question:
Adding onto what Driftxsequence said; basically we have two trigger wheels (spin inside the cas) that we need to get a signal off of instead of just one like most cars. Megasquirts (other than MS3-x) only have one VR conditioner, which makes the signal readable to the brain in the megasquirt, since we have:
two wheels=two signals but only one conditioner

you need to add another one.

Either buy the Zeal board or solder it together yourself as per the writeups, it is simple enough.

Here's a way more indepth explaination that what I gave you about VR conditioners.http://www.diyautotune.com/tech_arti...t_vr_index.htm