I bought this 1999 bigbear 400 professional or (1998 Kodiak) recently and took it for a run last weekend. I just putted around in second gear and I could hear what sounded like slapping in the topend. I just checked the timing chain and it is ok I'm no where near the end of the adjuster but I reset it anyway. I checked valves and they are spot on. I am getting a lot of vibration through the plastics just off idle. I can't figure this one out.

 

I've had quite a few bikes in with a "top end rattle" lately and all have been a light piston seizure causing piston slap. Even had a Honda 420 traded in with this, never known one of these to seize before. Yamahas have an engine balancer which is difficult to "time up" correctly, yours could be timed wrong.