This is a little bit strange in the fact that most times that I have done a new top end, the jetting may seem slightly richer afterwards.
1. I would give the carb a really good cleaning to make sure nothing is plugging up the pilot circuit and making it lean at idle. I can't hardly believe that the jetting could have changed so much that it would be reving that high, not if the jetting was correct before the rebuild.
2. Have you tried spraying brake cleaner behind the mag rotor while the engine is running? If it changes the speed of the engine then the left crank seal is sucking air. Just be real careful doing this one - spining parts can bite you!
3. To be honest it really sounds like an air leak somewhere or a carb slide sticking or hanging up. With the bike shut off, if you roll the throttle open and then let it go, can you hear the slide seating back down in the carb? Make sure that slide isn't hanging up!