Did it just start doing this all of a sudden, or was it after you made the mods you listed? If it ran fine before and just started doing it, I would look at the stator and electrical. If you just installed all the mods and it started, you may be a little lean. I havent jetted pro circuits, but with T5s and K&N, 290s are not big enough at sea level.
EDIT, have you checked for air leaks?