After the engine is up to temp pull in the clutch and give it a little rev. If all as smooth then put it on a stand, strap it to the floor (just in case it comes off) and rev again. If there is vibration with the tyre moving then it is most likely the tyre.
Have you changed anything else. I am not sure what kind of balancer this motor has in it, but I have had counter balance shaft bearings go bad in my 2 strokers before.