The only other big problem that I know of is the black box. Those are fixable.
Not all of the time, but a few people have had good luck. I'd say it's 1 in 3 that don't, but it's hard to say if thats because of the unit itself or errors in the process.
Carbs are the other big weak point, as previously stated. They are small and tend to clog up easily, doesn't help that the stock 400 doesn't have a fuel filter. It's really recommended to add an inline one, it really does help.
GSXR forks and rear shock are the way to go! The big question I'd be asking is if the front was swapped just for the upgrade, or if it was swapped because the bike was wrecked. Wrecked bikes aren't always bad, but they do mean you should really pay close attention to all the welds and the frame alignment.