Starting from the simplist and working back, did you put the airbox back on it with a foam filter? These bikes will not take the throttle without the air filter (short of some major rejetting).
Assuming you knew how to rebuild the carbs and got all of the seals and orings back in correctly, this sounds like a lean fuel condition (like the others said, water in carbs, air leaks, still plugged fuel passages, etc). These carbs have the smallest holes I have ever seen in a set of carbs and they are notorius for getting clogged by the particles slightly smaller than nothing.
If your bike was sitting for a while, it is likely the tank has some rust as well. Be sure to get an aftermarket inline fuel filter to make sure the fuel is clean to the carbs, otherwise, you will wear out the screws cleaning the carbs.
GSXR400 Racer has offered to help out someone else in the forum out by rebuilding their carbs for a nominal fee. Probably would be money well spent given his experience with these motors.
Good luck and keep us posted, carb information is always worth posting.