did you replace the spring/s inside the carbs? Did you use "mikuni" parts, for the rebuild?
If not mikuni, the "red dot" on the diaphramis too long, holding your needle up some, enuf to flood the motor at idle/bottom end. If you replaced the spring, then your "pop-off" is too low, and opening before it should. I recommend you install the stock one back in...If you answered "NO" to replace spring, and "YES" to mikuni parts, then I say, your needle is sticking, and or turn your idle up more...3k out of water...:cheers: