Thanks for the reply JeeperDon.
Here are a few pointers from when I did my GM into Jeep swap...
I subscribed to AllDataDIY.com for both the doner vehicle and Jeep year, so I could see "Jeep red with white stripe connects to GM blue with green stripe", etc..
I have the Mopar factory shop manuals for my Jeep, that is where I am getting my info on the wiring. As for my donor it was a drop out (engine, transmission, PCM, TAC, wiring harness, gas pedal, and fuse block) didn't have the complete vehicle. I got the wiring info form lt1swap.com to assist in making the wiring harness.
I eliminated completely the YJ under hood fuse box, only used the GM. The YJ block mainly had high amp body things that needed to be moved, and there are plenty of unused high amp fuses in the donor fuse box (power seats, HVAC, etc.).
Yeah, didn't think of doing that.
I trashed the fuse block when I completed my wiring project. On my wiring harness I have a small fuse block with a fuel and starter relay. But then as I was taking the Jeep fuse block off I started thinking of keeping it and integrate into the new motor wiring.
I had to have the GM PCM flashed to eliminate the VATS and most any other code that deals with things not on the YJ, like fuel tank pressure, after cat O2 sensors. I told them, "Just leave working whatever it takes to make the motor run right."
My PCM is getting programmed as we speak, should get it back next week. He is removing all the emissions junk, VATS everything except what is need to run the engine.
I used a Dakota Digital SGI box to send the VSS signal to the GM PCM, which likes to know if the vehicle is moving or not.
I'm using the Advanced Adapters Trans to TC adapter that has the 40 pulse VSS sensor to run the PCM.
You might need another SGI box to get the V8 GM tach signal to work right with a I4 YJ tach. I did until I changed to Autometer gauges
I may need to look in to that if I'm going to try to keep my stock gauges. I looked into re-gauging my Jeep in the beginning, but wanted to stay as stock looking as I can keep it. I may have to end up doing it anyway if there isn't a viable way of getting the gauges to work with the new setup.