Lets see, you will need: a new fly wheel, bell housing, clutch assembly, slave cylinder, transmission, modification to transfer case maybe, new rear driveshaft, peddle assembly, I think the computer is different, and im sure a few more things are missing. As for price, depends on how good the junk yards or Craig's list is by you.
Now the reason most people don't do this conversion is because autos are far superior to manuals off road, and in most every other situations. It just happens that the jeep autos aren't the best from what has been written.
I know a lot of things, most of them are only correct in my own head...
Better to be judged by twelve then carried by six. I'm sure this is going to get me in trouble down the line