Have had my '98 SE for a year now, been happy with it for what I use it for. Works fine offroad and the casual sight seeing rides into the mountains. Have no need to run it over 60 mph but have had it up to 70 a time or two.
Normal maintenance so far, bought it with 3000 miles on the motor rebuild with invoices to prove it. Since then I've replaced all the sensors, the water pump, fan clutch, serpentine belt, belt tensioners, the alternator, entire exhaust system and, the injectors will be replaced soon. Just because those are things IMO that should be done with an engine rebuild and weren't listed on the invoice.
One thing that the 4 bangers are known to have problems with is the exhaust manifold cracking and the two manifold studs in the head can fall out or break. Easy enough fix though and not expensive to do either. Chances are the ones you're looking at have been fixed, the 6 cylinders have the same problem though.
When he was a teenager he had a YJ with the 4 cyl and he often comments on how little power it had. He then put 31" tires on it and found that 4th and 5th were about the same, he couldn't really accelerate in 5th. Then he went to 33s and he said 5th was just about useless. I guess that's why he like to drive my TJ, it reminds him of his YJ except it has more power.
If you plan on running a tire any larger than the stock 27" tire it's even more crucial to re-gear a 4 banger to keep the motor working in the RPM range that it was designed to run. Can't recommend 35" tires for the SE they are too big and heavy for that motor and unless you dump a bunch of money into changing out the D35/D30 they can not be geared deep enough for that large of a tire. 33's on the SE for offroad and mountain driving will require 5.13 gears, 4.88's are ok for flat land but you won't be happy with that gear in the mountains.