the early ones ( 96-97) had a few head gasket issues, most of those have been fixed, my (late)'97 lasted 200k before the head gaskets went, still had the composite head gaskets on it ( the failure prone gaskets ) new gaskets are MLS ( multi layer steel ) and last presumably forever. ( new ones in mine are MLS ) I got lucky and caught the failure just as it had happened ( wife drives it, I check all fluids weekly, found low coolant and went from there diagnosing and found #6 cyl had coolant leak ) it didn't over heat so no head issues.
Timing belt, if it's not documented, plan on that and water pump soon after purchase. though it's not real critical, it is NOT an interference engine. BUT if the water pump fails and it does over heat, you'll be looking for heads. ( not cheap ) Use Toyota RED coolant, don't mix with green or with DEXcool orange
5spd Runners were built until 2000, then auto only
trans coolers in the auto radiators tend to blow out with age and fill trans with coolant ( search "strawberry milkshake" on the Toyota truck forums) if it hasn't been done, plan on swap to external cooler.
Runners came with 15 and 16" wheels, bigger wheels mean bigger brakes, it was mostly SR5s that were 15" wheel
mine is a '97 SR5 5 spd, non-locking rear, was equipped with 3.91 gears from factory, the rear diffs are known to have pinion bearing issues ( relaxed crush collar, bearings get noisy ) mine had been rebuilt, but the 3.91 gear is hard to find and super expensive compared to the more common and readily available ( and much cheaper) 4.10. Mine had still has a 3.91 front diff and a 4.10 rear ( i have a 4.10 front, just too lazy to change it, I don't use 4wd much and have the front diff actuator on a switch so I can use low range without engaging 4wd, makes moving trailers around a breeze )
I average 18-19mpg in mine, when I'm driving, about 14-15 when pulling 3500lb camper ( wives mileage is a little lower, she forgets to go into 5th gear )
Ride is decent, early 3rd gen Runners had recall on rear springs, mine had the recall performed with updated springs, they still sagged ( sitting on bumpstops unloaded ), I replaced with a set of MOOG rears, have KYB Gas A Just rear shocks, fronts were new strut/spring assemblies I bought off Amazon, being an SR5 it's lighter than the Limited ( less sound proofing and other crap ) so it sits up about 2.5" higher than stock, which I like, I use air bags in the rear coils for hauling the camper ( 450lb tongue weight )