Recall on the denso ignition coils on all 2003 R6's. Go to your local yamaha dealer and get them replaced for free with the newer mitsubishi coils. I think its technical bulletin 2003-016 or something like that.
Edit: D'oh! Didnt read your post fully, get the coils changed anyway
Edit: D'oh! Didnt read your post fully, get the coils changed anyway