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There is one wire going to a manual transfer case. Its for the transfer case shifter position lites on your dash, I think. You know, 4L-4H etc. I think that was one of your questions?
Well some said that 2wd and 4x4 has a different transmion wiring harness but there the same Trans with just different tail housing. I'm not seeing the difference. I have been wrong before!
When I put my tranny in I also bought a new wiring harness. It has at least 6 or 7 plugs on it. One goes to the transfer case, and mine is a manual t case, manual hubs, auto tranny. Look in my album. There are real good pics of the tranny and transfer case sitting on a jack all bolted together and ready to go in.you can see the tail piece on the trans before I bolted on the T case, Its black. I'm not sure if you don't see the diff in the trannys or the harness. But you can see both in the pics. Hope they help.