04 4.0 auto to manual swap

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?
 
What has anyone done here for cps? I was told they are the same from 42rle to nv3550 and they are definitely not. I swapped in an nv3550 into my blown 42rle and am stuck with how I want to tackle cps. The connectors are different. My thought was just pull the connector off my 2001 manual and unpin it and install it on the 2003 auto. Curious though how others have gotten past this and reverse? Trying to keep things as factory as I can