If you want to get a quick handle on what will fit, take a few minutes at
www.crutchfield.com and use their "what fits my vehicle" link to check things out. Most of the head units will go right in, and I seem to recall that most XJ's use 5.25" speakers fore and aft.
Not that that means anything - what you want to wedge in there depends on how much work you want to put in. I've got 5.25" speakers up front and 6x9's in the back - it's just a matter of putting in a little work with a Dremel! That, and some planning...
OEM wiring is fine for nonamplified speaker signals, probably up to a 50W head unit. Anything past that, and get used to the idea of pulling some heavy-gage speaker wire.
I've used Sony Xplod drivers with good results, and I put JVC poly-cones in my wife's 89. I strongly suggest you stay away from "paper" cones - they tend to get beaten up pretty quickly. Also, given the environments Jeeps tend to see, you probably want something that won't get waterlogged too easily.
Aplifier mouting poses a problem - not due to room, but due to security. The only effective way to hide an amplifier is to find one small enough to go under a seat (and find a way to provide it with cooling air) or build a false deck for the rear section and stash the amps under that. I'd give you a design, but I've not finalised one yet...
Pretty much any name-brand head unit will do better than what you have now, but I suggest you look for a few features to allow for future upgrades...
CD-R/CD-RW playback
mp3 decoding
auxiliary audio input (front or rear, at your convenience)
Pre-amp outputs (for a subwoofer, at least. three sets is better - use them as you need them.)
With a little looking, you can find a DIN-sized unit that accepts both cassettes and CD's (if you need it) or a cassette unit with CD-changer controls. Also, Kenwood makes their "Music Keg" which looks promising, and most of their head units will control it remotely as well. Just something else to think about...
5-90