I did that exact swap on my previous '97 TJ. The easiest swap is the the 32RH which is a bulletproof 3-speed automatic. The 32RH was used in the TJ '97 to '02.
Basically beyond the obvious parts needed, you also need to swap in a new engine computer set up for a '97 TJ 4.0L and automatic transmission so the automatic transmission's lock-up torque converter will work properly. You will also need to install a replacement longer (extended) output shaft seal into the 32RH so it won't leak where the transfer case input shaft seats in the transmission. The t-case intput shaft is too short for the 32RH so the new extended output shaft seal for the transmission fixes that. You can get that extended seal from Teraflex, Advance Adapters, Summit Racing, etc.
All the wiring is already present in your TJ, no need to add or change any wiring. So is the transmission cooler, that is part of the normal radiator that Jeep installs.
Finally, you don't have to remove the clutch pedal if you don't want to. I welded a piece of steel between the brake and clutch pedal so I could use the clutch pedal as a brake pedal for my left foot while rock crawling.
I'd be happy to talk with you on the phone if you run into any snags on anything.