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I think tomsn16 had a fairly fresh used harness for sale, but it may be gone now. You are likely looking at about US$1300 for a unused new harness, if you can find.
JDM versions run about the same, but they may not be a perfect match (less emissions wiring).
The emissions harness has a leg that runs back to 3~4 sensors at the far end of the transmission.
Often this is missing from used harnesses, as people cut it off, because it is a bother to unclip the connectors that are halfway under the car.
A complete set of new solenoids will likely run about US$750 and likewise the full set of formed vacuum hoses.
Most people will not go for factory vacuum hoses, but they look sharper and help you hook everything back up correctly.
Here is one of the least crispy of the 10, or so, used emission harnesses I have. You can likely find used ones like this for $100 (or free). Often some of the connectors will have been scavenged off. This one has the length with the transmission sensors still attached.
This harness may be from a newer version JDM. Newer JDM had a "solenoid box" at its core, rather than the rats nest. (see "rat box' in top corner of the pic.)
It also looks like Atkins Rotary has the harness for around $1500. I knew going into this that it wouldn't be cheap, and let me tell you, it isn't.
Since the current harness works, I think my current plan is to get a replacement for the next time I pull the motor, put the new harness in, and work on rehabilitating the current harness. At least that's the plan now. I can tell from driving the car that I probably should've got new rotors and housings. I don't feel like the compression is where it should be. But this is all from the seat and I'm breaking the motor in now. Hopefully after 500 or so miles, it improves and I'll check the compression numbers again.
A smoke test is a good idea and I wanted to find someone/someplace in NorCal to have it done, for that reason exactly. I need to get a water temp and boost gauge for the car so I can monitor both those parameters more closely (since I've read about the stock WT gauge in the car.)
I just noticed there is an oil leak somewhere towards the back of the motor, driver side. I'll jack it up this weekend but I used Hondabond on the oil pan gasket and got an oil pan brace with a new oil pan. I also let it set for 2 weeks, so it should have been good to go. I'll know more once I check it out, but always one thing or another, right?