There are only a couple of things that come to mind. If you get a V6 truck, the headgasket recall needs to have been done, which you probably know about. The other is that there is an active recall on the steering relay rod. This on an IFS goes between the steering box, idler and the two tie rods come off it to the steering arms. Toyota had some that apparently had bad metallurgy and could fracture, so if you take it in they will give you a new one. For free. You might also get a free alignment, which is nice. There is no mileage or age restrictions, a 15 or 20 year old truck gets a new steering relay rod. Nice.
Despite all the Internet wisdom, the '86-'95 IFS trucks are excellent values. In stock form they are just as reliable as any other Toyota. The IFS gets an unfair dink, but it's fine for what it is. Yes, it gives up some simplicity and articulation to the solid axle. No argument. But comparing stock to stock, the stock solid axle and the stock IFS aren't that much different in wheel travel and IMHO the stock IFS rides enough better that I hand's down prefer them as run around trucks. The problem with IFS is that there's only an inch or two of easy lift and not a lot of easy wheel travel to be had, where as a leaf sprung truck is easy to get 4" of lift and make a better crawler. But I got my truck through the Rubicon last spring, so IFS being completely unsuited to rock crawling is bull. If you are building a dedicated rock truck, sure, solid axles. If it's a mixed use, daily driver, a little rocks, lots of dirt roads, well I have stuck with IFS for a reason...
Personally, I think Toyota nailed it with the 3rd gen trucks, but each of the first three 4WD gens have their pluses and minuses. What is common is a relatively simple engine and drivetrain, straight forward design. All '79-'95 trucks share similar layouts, but the reason I think the '89-'95 trucks are the better is that Toyota licked the rust problem for real.
For an idea of what I think a great daily driver, weekend fun truck could be, I think what Steve Schaefer at Sonoran Steel built for his shop truck gives you a nice starting point. Mine is set up quite similar, just a few differences in the front suspension so that I can run 33" tall tires. But for a very reliable IFS truck, I think you only need to do a couple of things from stock. Add a rear frame truss and beef up the idler. That's really the only mandatory things that I think IFS trucks need. Otherwise, one of Budbuilt's low profile transfer case cross members is nice to gain clearance and get a real belly skid and some armor as fits the need.
http://www.yotatech.com/f86/sonoran...4wd-mini-pickup-featuring-mighty-28-s-104077/