The primary clutch on Polaris's make to that transfers the noise throught the crankshaft too. I know on my 700 thay had a rubber bumper for a header sapport an it melted away ab made alot of noise so I made an new one out of silicone an now is quit. The clunk in the trans I think is do to the drive turning slowly an then stoping when shifted in.

 

the primary on my 400 has never made any noises. this is a faint tick,tick,tick,tick,tick

 

mine has 4700 miles on it and it has made the noises from day one. the motor on mine has never been touched.

 

Drive it and don't worry about the ticking or the back lash in the tranny as mine has done the same thing since new. With just shy of 10000miles (780hrs) I have never touched the motor or tranny.....