Stic O I would be happy to talk about the 4.0L wiring I did, I also updated the 88 to use a 93 power distribution box under the hood.
The way I build a 4.0L conversion harness (or any conversion harnesss really) is to use the 1988 plugs that used to plug into the truck (at the firewall, from the 2.9L PCM and power dist harness) Then, re pin them onto the end of the new 4.0L harness.
the 4.0L harness is stripped of anything not needed in the BII (BII already has headlight wiring, fuse panel under the dash, you dont need daytime running lamps or 4WABS brakes, you may want to remove the cruise control and AC, etc), re pinned to match the trucks wiring useing the original plugs and blamo you have a better then factory harness.
The key is to make a complete map of the truck and then of your new PCM, engine and trans harness. I went a step further and replaced the BII crappy relay setup with the 93 power box and power distribution, alternator wiring etc. This makes it real easy to go back and add things like an electric fan, heated seats, stereo, etc later and its integrated into the factory harness
Does that answer it?