I have been chasing a similar problem for a while. The engine sometimes took some time to return to idle at a stop and between shifts things could get lumpy as the engine hunted around for what RPM it really wanted to be at. Finally found the right guy who was a former S&S-sponsored racer who said my TPS (Throttle Position Sensor) needed to be adjusted. He manually adjusted the sensor while watching the readouts on the S&S software and my car is back to a perfect tune. I guess there are throttle stops that wear over time and can throw things kind of out of wack. You can't visually confirm anything is worn, because the throttle snapped back and close perfectly. Except my RPMs were not decaying to an idle and RPMs sometimes remained high between shifts. Hope this helps.