i just wanted to share the news for those of u who dont know. I bought my bike about 5months ago with an idle problem. I would give it gas and it would stutter really bad, I changed out the, plugs, filter, added fuel cleaner and to my advantage my Yamaha tech informed my that there was a 2 recalls on these bike, one was the coils and the other I dont rememer, but if u have a similar problem call ur local yamaha and give them ur VIN# they should bring up ur recall and fix it for free. Just thought id share this!
I ran into the same problem. Had my 03 for a year and put 8000+ miles and then all of a sudden started to act up. Didn't know what was up and did the same things you did until finally took it to a guy and he told me it was the coild and then found out there was a recall for them. got a new set from the dealer and problem was fixed