Mine was doing the same thing, I put it in the shop and what they found was. Yamaha sets the air/fuel mixture slightly rich from factory to make the bike run cooler during the break in process. After break in you take it back to the dealer for the break in tune up... the air/fuel screws have a cap in place so they canĀ“t be messed with until after break in. The dealer is supposed to drill out the caps and re-adjust the mixture settings. Once the valves themselves get a little wear on them, having cylinders not buring clean leaves slight back pressure while the exhaust valves are trying to come open, it creates a chatter noise. The drilled the caps and adjusted the mixture and my chatter was reduced to a very slight one.
Thats where I would start... check to see if those caps on the carbs were drilled out...if not, its probably the problem on your bike. I might also check the tension on the Cam chain.