Its not that hard to do if you swap in a jeep tranny that is mated for your motor. I just did a swap on my yj from a auto to an ax15 and yes it is more challenging on the rocks but with the gearing and axles I am running I need mor that 3 gears
Your best bet is to go to a junkyard and pull of the parts you need from a junk jeep. you will need the slave cylinder and the brake/clutch pedal braket to start. you could alos grab the brake light switch that goes with it iirc it is different from auto to manual.