Be on the lookout for disabled air-injection systems; it's a popular modification, especially when aftermarket pipes are installed. This might lead to problems if your state has emission testing. There are also some reports of premature carbon buildup, but that's probably a function of the way the bikes are ridden and the quality of the fuel the owners are using.
Early bikes had vapor-locking issues, but enlarging the fuel cap's vent hole normally solved that.
Some owners reportedly had trouble with the countershaft sprocket retaining nut loosening up. Not to worry-a stout wrench and a shot of Loctite is all it takes to put things right, so don't consider it a deal-breaker.
Older models were also jetted notoriously lean, so a jet kit might be on the menu if the bike in question is bone stock and has a penchant for long warm-ups.