I've done this in my car.
My car is an early '89, so it has the same motor mounts as the '86.5-'88. The donor car was an '87. No problems with compatability there.
The chassis/GE harness was a grey plug. The engine/GTE harness was yellow plug.
The plug for the instrument cluster worked without issues, all instruments worked (Swapped out tach board, but my tach does read high.)
I had the following issues:
1. Headlights. As soon as the battery was connected, the headlights turned on. They did not flip up, just turned on. I removed the headlight relay until I could re-run the line. I ran a new wire from the headlight relay to the trigger line on the #2 headlight integration relay, and cut the factory harness line. I believe that this hides the headlight status from the ECU, so it doesn't try to idle up for the extra electrical load, but this hasn't caused me a problem.
2. ABS. The plugs were not compatable, however the colour coding on the wiring harness was similar enough. I cut the pigtail for the chassis harness on the donor car, and the ECU side harness from my car, and turned them into an adapter harness.
That was it for wiring issues, though of course all of the underhood goodies (Except the FP relay/resistor) were taken from the donor car as well, so of course the wiring harness worked with it.