well with the standard conversion, you'd need a new pedal assembly, another hole in the firewall, clutch master & slave cylinders, and obviously the new transmission itself. its quite a conversion and most people agree that its more worthwhile to just find a jeep with the manual transmission in it already
also, you wouldn't be able to use your remote start (as easily)...
that said, my first jeep was a '90 XJ automatic, and now i'm driving a '94 XJ 5 speed, and i love it. i'd never go back, the manual transmission is amazing on and off road, and it gets me close to 20 mpg when i drive it like a grandpa
food for thought