Allow me to offer up my 1/2 cents worth. At approx. 25,000 miles miles my 2005 R3 standard started stalling. Usually when getting off the highway and coming to a stop. Initially, it would would just idle real slow and rough (500 rpm's) and then recover. As time went on it would actually stall. Here is what I did to fix it (has been good since, has over 50,000 miles now). On the left side of the throttle body assembly there is a mechanical stop screw. It's typically painted yellow to indicate tampering. There is linkage between the mechanical stop and the throttle butterflies. When you are running "on throttle" the ecu cuts the idle stepper voltage to zero because it thinks the engine is "idling" to fast. My linkage had worn to the point that it was allowing the throttle butterflies to close completely. When I would come to a stop, the engine would starve for air until the idle stepper got the butterflies opened up again. I believe the engine should have a "base idle speed" of maybe 650 rpm's with no intervention from the idle stepper. I turned in the mechanical stop screw until I could get off the throttle without it bucking and stalling. Now you might ask "why would my brand new bike have worn throttle linkage" ? I'm sure it doesn't. What could be happening though is the "base idle speed" could be set to low from the factory. Maybe trying to meet some emission standard or something. As the engine breaks in and loosens up a bit the problem sometimes takes care of itself. Other times not. I would say if you have more than 10,000 miles and it's still stalling, and the dealer is still scratching his arse, I would give the throttle screw a try.
