It could be anything, or a collection of a lot of things.
Proper jetting would be a good place to start.
How long since the top end was rebuilt? If it has been 9 years your top end might be shot. A new piston & rings could do wonders. It could also need a valve job. If nothing else, run a compression test on it.
Have you adjusted the valves recently?
If the bike is bogging down during a sustained run then I would also suspect a fuel delivery problem. Try cleaning the carburetor. Make sure that the screen inside the gas tank isn't clogged.
There are too many possibilities and not enough information for us to really help here.
Rod