Join Date: Feb 2009
Location: Parkville, MO, USA
I read a few pages back and couldn't tell if you'd cleaned the throttle bodies when you had the air filter off. A black ring can form where the butterflies close against the TB walls, and this can plug some tiny air passages. I've had to do this a couple of times on my STs (just a couple of weeks ago, as a matter of fact), and it clears up the exact same symptoms you're describing. It doesn't fix the root cause, but it fixes the problem for several thousand miles.
2006 ST3s ABS, 1991 Suzuki GSX-R750
2000 Yamaha WR400, 2003 Honda TRX300ex