I know this is an old thread but I’m currently doing this same swap. Mines a 2000 Tj with 4.0 auto 42rle. A friend of mine had a wrecked manual and gave me the engine and trans out of it for free. Wiring harness and all are with the engine. It’s an 04 Tj 4.0 with manual trans. I’ve bought the pedal assembly and slave cylinder set up for it. But now from what I’ve read it’s not going to work once i get set up Bc of skim?