Update:
Well the NY dealer called and said the bike was finished so I drove 2 hours to pick it up.
They said they had checked a number of things including the compensator and said it was way out of spec and replaced it.
They were sure they had the vibration and the engine noise fixed.
The disappointing thing is it didn't fix the vibration or the engine noise. It made it better!, but it still vibrates.
When I got back from driving the bike for 2 hrs at 3000 RPM I could barely feel my fingers and it took 30 minutes to get the feeling back.
The dealer tried their best to find the vibration but it is still not acceptable for long distant rides. But they did cover everything under warranty.
Sooo.... I guess I will pull the motor myself this winter and send the crank out to be trued, balanced and welded.
So far I have spent 90% of the mileage on my bike travelling to the dealers and back. They have worn me down!