Are you bench synced?
Did you set all the idle mix screws to the same start point?
Did you ceck to make sure all of the idle mix screw parts are there and installed in the correct order?
Did you set the fuel level in the bowls?
I would also hghly recommend relocating the CDI to the top of the air box when you replace the coils. It will be much cooler and more protedcted from the elements there.
I would also recommend updating the fuse block.
Keep in mind also, these bikes will not run right with air box open. They will idle, kind of, but bog and choke with any throttle.
Hanging throttle, stuttering/bogging on wind up, back fire on decel are all indicators of the carbs being out of sync. Of course they can also indicate other problems, but the sync is the most likely culprit.