The auto tranny is the weak link, as long as it's OK you're probably good. An auxiliary cooler is a good idea - pay $200 now or potentially $2000 later to fix the tranny.
Finding the 5 speed/rear locker combo is very difficult. 5 speeds also command premium prices because they're more rare. SR5/Auto/3.4/rear locker is a fairly common combo, so don't think you need to get a Limited in order to get the locker.
In 1999 Toyota started putting some interior upgrades: 3 12v power outlets in the dash, cup holders in the center console instead of sticking out of the dashboard, auto-off headlights (keeps you from accidentally running your battery down) and a few others. The 99 models also are the "highest" suspension from the factory - starting in 2000 they began cutting the suspension height because of the fear of rollovers.
"Sport" or "Highlander" models are SR5s with a few cosmetic additions, most notably the hood scoop. They tend to be highly desired by 4runner fans, though, so you'll have to decide whether the scoop is worth the extra cost. It wouldn't be for me.
Limited models have leather seats and sometimes (but not always) a sunroof. 99-00 Limiteds have the multi-mode transfer case that gives you full-time 4wd for the highway, and they quite commonly have lockers as well. The 99-00 Limited is the only 4runner that has the multi mode T-case + the rear locker except for the 09 Trail Edition that was introduced briefly at the end of the 4th gen 4Runner's run.
96-98 Limiteds and 96 - 2000 SR5s and base models have conventional 2wd/4wd with the J-Shifter.
All 01-02 4runners are 3.4 Automatics. No 4 cyl option, no 5 speed option, no locker option. They had traction control and multi-mode T-cases in all models.
You can get more information at the 3rd gen sub-board over at
http://www.t4r.org.
, and hood with scoop also a plus from my view. Body is good overall, nothing but a few scrapes on the bumper and a couple door dings