Any more info on this? My 2004 started doing the same thing. I cant imagine that it has anything to do with the starter because every time its happened I have been riding for more than 15 mins. It typically happens at traffic lights, sometimes early in the ride and others after an hour. It's Florida so its hot and high humidity. First thought the engine cut off switch but that checks out. Then thought ignition but that checks out. Battery is 1-1/2 yrs old and the stator+rec was replaced 1-1/2 yrs ago.
Thanks for any help in troubleshooting.
IIRC, Mark found the wires going to from the Pickup coil under the clutch cover to the ignitor, were damaged. He found a really crappy tape job where the PO
tried to put it back together. When he found the mess and fixed it, it cured his problem.
Pick up coils are not one of those things that commonly go kaput, but we have seen it a few times on here over the last 5 or 6 years. There is a check for it in the service manual. There is a connector behind the left side cover. You could trace the wires coming out of the clutch cover(a two wire connector)and make sure the connector hasn't come loose, or the wires worn through somewhere.