I the dash harness in my MJ with one from an XJ. It may not apply to you, but for my '92 i had to make two changes to the harness. The '92 XJ had to connectors that ran wires back to the cab, the MJ one. Move some of the pins over from one to the other to match the cab connector on the MJ. I also had to run a wire to the steering column so my brake lights would work.
Your best bet would be to find one from the same year and motor, don't think tranny and tcase make a difference. Definitely a good idea to have a FSM or some wiring diagrams around. Someone posted up on comancheclub about needing a harness, i'm guessing it was you. If there ever is a time to get power windows and doors, its now. Find a loaded XJ, pull all the wiring, door lock motors and window regulators and move them over to your mj.