2000-2001 has the 0331 head, which due to a casting defect (in some, not all) can cause the head to crack, causing coolant to get into the oil which could cause engine failure. How you ID the 0331 head, I still have yet to find out. Someone more experienced in the matter should be able to help with that.
New shocks can be found from many suppliers, but 9 times out of 10, the cheapest route ( for me locally anyway) is Monroe, around $30-35 a piece. Make sure you know that they fit before buying.
As far as the fan switch goes, use a voltmeter to check for shorts.
Anything to break?
AC vents (possibly). Mine lost a small tab on the inside that allowed it to move up and down.
Fog light lenses. I have seen many XJ's with cracked ones. I have been told by some that it could be considered improper equipment, but I haven't been pulled over yet, and mine also passed inspection.
Center console latch. The tab on the inside just broke off one day. Just something that happens.
Another thing is the drive shaft making a clunking noise and jerking when accelerating after a coming to a complete stop. This link right here will help you with that. http://www.jeepforum.com/forum/f11/g...ite-up-357569/
As far as the lift goes, 3" isn't too difficult. Make sure you use common sense when jacking up the vehicle (like using jacks and jack stands that are recommended for the vehicle's weight) Regearing is more than likely recommended, because of the increased tire size. Once again, more experienced owners should be able to help.
Hope I covered most if not all of what you needed help with.