I think it was a air leak. I swapped out the gaskets for exhaust and engine intake and made sure the nut where nice and snug. Took it out for a spin and so far and not holding my breath on this but it's running normally. I need to take it out tomorrow for more testing to be sure. I got it up to 38 with out allowing it to go full throttle. The rough riding is back and it's just the rpm's the engine has that is causing it. If I lower them to the point where it's not rough the engine idles to slow and stall's.