I have a much more interesting (and tricky) wiring situation that I'm going to post about in a few days. I feel that you might be able to help. I'll PM you when I put up the thread, if you don't mind. Here's a quick summary anyway:
I'm installing a '94 4.0, '94 4.0 PCM, & '94 wiring harness (all from same donor) into my '95 2.5 YJ. Everything's going great, but the wiring layout at the 16-Way 'Engine Wiring Connectors' (ENG-1 and ENG-2) do not seem to match between my 2.5L body harness, and the 4.0 engine harness. I haven't been able to really get into it and determine which wires match the '94-'96 FSM Wiring Diagrams (as below).
I got the motor to run, but I had to run a jumper to the ground of the Cam Position Sensor (Distributor Pickup). The Sensor Ground from PCM Pin #4 (K4) does not travel through ENG-1 and/or ENG-2 as it should. In the engine wiring harness, the K4 ground connects to the VSS, the Cam Position Sensor, and then runs to ENG-1, but at ENG-1 it does not mate to a ground in the body harness. Ever seen that? If not, no problem, I'll post with more details & photos when I can. Thanks.
Edit: Also, the donor had ABS, but my Jeep does not. It probably had AC as well but I can't check right.