The standard rust spots on mine are:
front driver corner of the roof, below the gas cap, bottom of the doors, inside the lip of the front doors on the body looking up when the door is open. If Jeep had put a better seal between the roof and side panels half of the rust would be gone.
Mechanical
If the AW4 auto transmission hasn\'t been over heated its good. When I was shopping of my XJ I must have driven 20 of them, every one had the shift from neutral to drive engagement clunk, but it never got worse on mine so I ignore it.
They put a few wire splices at the door so the power windows and front speakers can get flaky over time.
But given all that IMHO a used xj is the best bang for the buck in the 4x4 market.
If I find a good price on a used 4dr KJ Rubi I should be selling my xj.