Have you checked the reeds ? When they are chipped or cracked it will cause the bike to sputter on the topend as you are describing alot of times.
I also had a bike that I pinched the coil wire on. I pinched it between the frame and the radiator in a fall ,and it didn't look that damaged , but it was and it caused the bike to run like crap as the rpms went up. What a nightmare that was to diagnose.
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