The quick answer is A Lot!!!! The swap is not just a simple drop in a 4.0L and go. Most of the folks I have chatted with about the swap (i have a 4 banggor 2) said many people ditch the project half way through because it is so much work.
A few thing you will need to swap, 1. axles, unless you have a very and I mean very light foot, 2 if your Yj is newer one then the CPU will need to be swapeed to,,,, plus a hole list of things,

There are a few mod's you can do to your YJ, if your going to use it to drive back and forth to school, you can down size the tires to no bigger then 31"
Some say a bored out TB and sapcer with exhaust, jet chip. etc help, (oh boy I am sure I will get and ear full for that one <img src="/forums/images/graemlins/lol.gif" alt="" /> )

Oh and I forgot the last Mod you can do, just buy a jeep with a 4.0L in it
cheers
Mud