4.0 ZJ's (93-98) this is what I've observed as common problems on this generation after 100K.
Cracked exhaust manifold, appeared to be a [censored] shoot. Easy to check by just sniffing around under the hood.
Clogged CCV system, equivalent to a PCV system. Have two orifices on the valve cover that are notorious for clogging up on vehicles run on to long of oci's. These are a bit of a pain to remove with out breaking. Not really sure how to check if your just checking out a vehicle to buy.
Worn out steering box, usually an issue with neglected fluid. These can be adjusted to some point to tighten up again but it'll never have the super tight steering it once had.
Worn out tierods and balljoints if it doesn't track straight on the road after tightening the box, look at getting these replaced.
Common leaks include the oil filter adapter on the passenger side of the block, the rear main seal and the valve cover seal. All relatively easy to take care of and can be checked for by crawling underneath and looking around by the oil pan.
Rusted out rocker panels, might not see it at first (I know the Laredo's have plastic trim covers) but you can easily tell by crawling underneath and looking at the pinch seams. It'll start getting nasty quick. A oil or wax based spray lube can prevent this and or stop it from spreading.
If it has a Dana 35c then watch out for any strange noises. The bearings ride directly on the axle shafts and if the level isn't kept in check then the entire shafts will have to be replaced. Conveniently Chrysler opted for a rubber fill/check plug which is prone to seeping. Additionally look for leaks/seeping where the axle tubes meet the pumpkin. Axles (35c and 44a) that have been previously overloaded/hit to hard on the trails develop a leak at those junctions.
Trackbar and control arm mount points, rust just loves to start attacking those areas. Certain years had greaseable tierods upper balljoints, to bad 90% of owners didn't know that. The front driveshaft also has a greaseable slip joint.
Bushings, the control arm bushings can be checked for major play by coming to speed (about 30-35mph) and abruptly letting of the gas. Play in the bushings will allow a "shift" that you'll notice. Similarly if you accelerate from the same speed you may also notice a shift. If you hear front end clunking/bumping then check the front sway bar bushings they may need replacement, can easily be seen by crawling underneath the front (2 clamp style) and on the sides behind the front tires (two doughnut ones on the swaybar endlinks).
Loud noise from the front, like a wheel bearing? They are sealed unit hubs unfortunately, about $90 a pop. Can be checked by the good 'ol lift and wiggle test.
The 242 transfer case is usually preferable to the 249. The 242 has 2wd drive mode and is chain driven compared to the all time 4wd 249 which has a viscous coupler. The coupler alone sells for $300 and can last past 100K, but it's life is severely reduced if all 4 tires aren't the same diameter. Can be checked by doing tight "8" turns in a parking lot. Manifests as skipping/hoping when the coupler is toast.
Yeah the 42re trans is sensitive to heat and fluid condition. I'd look for one with a factory equipped tow package to better your odds, those came standard with an aux. trans cooler visible by peeking through the grill.
Vehicle information display center (on limited models) usually develops cracks on the circuit board or the plug pins become loose. It'll usually flash in reset mode if this is present.
Neutral safety switch, located externally on the side of the trans controls the reverse lights. If it's in reverse and the lights aren't then it's the culprit. Can be disassembled and cleaned though.
Crankshaft position sensor, this will definitely need to be replaced on anything with around 100K. It'll cut the spark completely randomly while driving at any speed when it's on its way out, a bit scary on the interstate.
If it's got high idle on start, easy fix, idle air control valve in the throttle body.
Driver door hinge pins, relatively easy to fix. Just common wear item appears as a sagging door that catches on the body.
Well that's the major stuff I can think of at the moment. Hope this helps you out and good luck.
