Originally Posted by Jerry Bransford
The wiring harnesses are the same between Jeeps with autos or manual transmissions. You shouldn't need to change or add any wiring for what you're doing. You'll also need to swap your engine computer for one programmed for a 5-speed. Your present ECM (engine computer) is programmed to look for a drop in RPMs once it signals the automatic to lock its torque converter which naturally won't happen once you get the new 6-speed working, which will generate a Check Engine Light. Make sure you get a ECM for a '97 with the same engine type and for a manual transmission. You can most likely find one at a good price on eBay.
By the way, as mentioned above, I converted my previous TJ (stolen last year) from a manual transmission to the same 32RH transmission you're removing. I miss the heck out of that 32RH 3-speed automatic, it was an awesome offroad and rockcrawler transmision. I LOVED that transmission... it makes me cry that you're removing yours.
Jerry, he's swapping in an NV3550, which would have never originally came in a 1997 TJ. Even though I know nothing about the NV3550, my guess would be there are some differences in the connectors.
OP, your jeep doesn't need anything from the manual transmission to run. I would get the transmission in and new/reflashed ECM set, then worry about the wiring. Or do some LED tail lights and forget about the reverse lights altogether.