For someone that has read and read, you didnt absorb much by the sound of it!
You need the whole harness for OBDII operation, thus a donor from the OBDII years would be much better. The "adding 2 wires for the 2 extra injectors" trick is possible when you are reusing the original wiring harness. Good for a 2.5 manual to 4.0 manual swap etc.
The transfer case is manual control only, with a few sensors to tell the rig to light the low range lamp, and a VSS. The AW4 is a computer controlled transmission, thus the TCU behind the dash on most XJ's.
You would probably be better reading up in the yj section, as there are MANY swap threads there. Never really bothered with the TJ section myself, didnt like the vibe there when I last visited.
1998 XJ on 37's.JK Rubi axles with chromo shafts and ctm's, 4:1 transfer case, etc etc etc.
2003 Range Rover HSE, 4.4 Quad Cam.
1998 Range Rover with a 6.0 LSx
1994 YJ, 4.3/700R4/OME SOA, etc
Western Star 4900EX 4 axle.
4.3/700r4/new frame buildup (YJ)....