Originally Posted by Pleiades

No harm in running some injector through. As mentioned - check the idle speed is >1400 rpm.

My gut feeling is it might be a TPS problem, especially given the vintage of your bike. Have you checked this in the dash's diagnostic mode? What is the start reading on a closed throttle and what is it at wide open throttle? Does it increase smoothly, evenly and consistently as the throttle is opened?

Have a look at these threads:

http://www.xt660.com/showthread.php?t=948

http://www.xt660.com/showthread.php?t=56