I'd say carbs, as it inproved when you gave them a clean sounds like there is still some crap in there and check the air filtter.
Make shoure you balence the carbs as well, the miss GSXR1100 dose this some times will tick over but pops and bands then dieds when you open the throtel give them a good clean out and a balence and works fine, some times you just get crap fuel when you fill up.