I have an 05, needed recall.
TPS was replaced by dealer 2011. Paint on screws was not on new TPS housing, so it was replaced.
Having the the same problems, but no stalling yet. Shutter. mis-fire when pulling away from stop.
I replaced engine a month ago, having transmission problems, used throttle body from old engine, idle up-down unstable. almost stalling,
Replaced TPS sensor today. Short test ride, no hesitation. Idle is smooth, forgot how it should be,
I don't believe Yamaha will cover it, 10 years old. Internet $ 150 or so. Updated part # Slightly differently looking TPS,
I had some issues replacing it, has tamper- proof torque screws. Lower screw is difficult to remove, frame blocking screw.
TPS will need to be set to proper setting after replacement, put in diag mode. 05 set to 15-17 fully closed throttle position.
Sounds like a TPS problem. Stalling, surge