go find a good race tuner.. dyno time. Short of that, you are asking us to basically "crystal ball" why your bike doesn't run right. Buy an owners manual, check some stuff, get back to us. Could literally be 1 or more of 1000 issues.
check the plugs?
measure resistance on the coils?
Sync throttle bodies by someone WHO KNOWS HOW?
measure fuel pressure?
Send your fuel injectors to www.proflowtech.com ?
Check valve clearances ? rough idle is classic symptom of out of spec valve clearance