From my experience with a 1990: Exhaust manifold cracks, radiator, water pump, door hinges, front seats (esp. reclining mechanism), windshield wiper linkage, wiring harness to blower motor shorts out, headliner sags, gas leaks at filler tube,and of course, the brake rotor recall.
I have 4 XJ's, 90, 96, 95, 00.
00- Turn signal switch(hazards come on with left signal)
00- drivers side window regulator=snap! 2x
00- cylinder head=snap
My 96 has been solid except the 1-2 shift solonoid, its my trail rig.
The 90 has no big issues except what has been inflicted by me.
The 00 is a money pit and has the lowest miles and has been babied
The 95 has had a couple of exhaust manifolds put on it
1999 : Console latch is okay, hinge screws stripped out. (guess I should stop cramming more crap in there)
Front Passenger window regulator broke (over a year of looking in junkyards for good ones I bought new)
All window will only roll down with Drivers control
Rear driver door lock inoperative
Oil fill cap stripped out
Driver seat broke (re-welded twice then got prelude seats)
Exhaust manifold cracked
Aux fan bearings crapped out
Pair of hub bearing units
And a Parking brake lever assembly stripped out
I'll probably never understand the Jeep thing, I may some day have brand loyalty to a manufacturer but I really doubt it will be to an "American" brand. There is a reason XJ's have low resale value and sometimes it worth a little extra to get quality.
I bought my 99 about 2 months ago with 93k on the clock. So far I've replaced the IAC, CPS, Coil, belt, tensioner pulley, 4 crappy sounding speakers, and cap/rotor/wires/plugs. I've fixed a leak on almost every window and a real nice one in the cowl that was leaking onto my fuse box. I've also got a bad upstream 02 sensor, a leaky evap core, destroyed control arm bushings, a crack starting to form on the manifold and I'm pretty sure the cat is plugged up. I've got all the parts to replace the entire exhaust sitting in the garage and I hope to get that done this weekend. Control arms can wait until I lift it.
She came with a whole stack of maintenance and service records and as far as I can tell, was real well taken care of. I guess the XJ is just rejecting me as a owner.
Don't get me wrong, I like my XJ, and even after I replace it as my DD I'll keep it. I don't mind fixing things, I just wish the problems had spaced themselves out a little bit more.
Nah, don't do that! Even a XJ that gives you trouble is still better than a Yota, and that IFS is junk, SAS is just too much money to put in a under-powered over-rated toyota. I was a toyota tech for 5 years back in the mid eighties, I have no use for them, I'll take a XJ any day.
I wasn't complaining about my 00' just that I've had the most trouble with it. Its never left me sitting and is now very dependable.
1998 classic: Alternator is place very low. Dirt and mud can get itself in there pretty easily and kill the bearing. I've seen a lot of people with sticky valve lifters (seafoam cured that for me!) Rust seems to build up in the same places in a lot of xj's too. A downside of having the 'classic' package is that the rear bumper has matching paint...gets really scratched up when trying to load stuff in the back. But hey...i wouldn't want anything other than an xj!
-Cruise Control
-Master window control switches on driver side door likes to "duck" into the door if using switches wrong since the holder is broken
-Rear hatch shocks
-NSS is somewhat sensitive
... Thats all I can think of.