I had a simular problem with my bike before I rebuilt the engine.
When sitting at an idle, if you tilt the bike over to the left (like it was on the side stand) do you hear allot of mechincal sounds? Bopping, grinding, ect...? That's what I had with mine. Turns out the engine had been apart before and the stupid mechanic didn't put the snap ring in to hold second gear in place (well, okay, it was there... but about 3/4 of an inch away from where it should have been). This allowed the gear to slide back and forth (and is one of the gears that shouldn't do that) causing all kids of lovely noises. Fortunetly, the only damage I could find was a severely worn out shift fork. All the gears were still good.