I have a '98 and it was damn near flawless when stock for 14 years.
Radiators are terrible, so hopefully that one has blown and they replaced with with an all aluminum one. They start to leak where the plastic meets the metal.
The air conditioner fan speed knob broke on mine once...< $10 fix.
Left blinker works intermittently...likely a connection issue in the stick. Very annoying.
Hardtop rear window, if it has a hardtop in addition to the new bestop, leaked a bit in heavy rain (still don't know where/how).
I had the 2.5L in my old YJ and it had a lot of starter issues...which I think were caused by mud caking it up...back in my young stupid mudding days. Just check for normal starter sound (that whine it makes).
They will all probably have a loud noise (creaking) from the steering column when turning in cold weather. It is a known issue that can be remedied with silicon spray, but you might be able to use it as a bargaining point. Again, very annoying when it does it.
Check normal stuff, belts, hoses, etc.
Good luck on that...great vehicle!