Just posted this on another board... thought I'd share it here....
Been looking for an opportunity to share my experience with my 2 non-starting RTs.
My 2003 acted up on a cool morning in the Smokies. All lights and indicators normal, would crank but would not fire. Jumped off another bike and it started. Worked fine the rest of the trip. Acted up again after I got home, intermittent crank but no start. A buddy present at a no start event asked if the starter always sounded so "rough". It started me thinking so I pulled the starter apart and found the shield sealing the reduction gearbox dislodged and was shorting out the windings on the armature. Fixed that with some JB weld, reassembled and the problem and noise went away.
The starter shield problem is documented elsewhere on this site.
Next bike was a 2004RT which I bought non-running, was told the HES sensor was bad. While waiting for a new sensor to be delivered I swapped various parts including the HES and starter (fewer miles) from the 2003. The bike fired right up. Once delivered I installed the new HES in the 2004 and all was good.
I reinstalled the 2003's original HES along with the starter from the 2004 and suddenly it would not start reliably. Figuring I damaged the wiring on the HES I ordered another one, installed it and it still wouldn't start reliably. Many hours of hair pulling later I yanked the starter for lack of another idea and found the same dislodged shield as I found on the 2003 while in the Smokies. Removed the shield completely and all was good.
So... the shield shorting out the armature windings pulled enough voltage while cranking that the ECU was not getting what it needed to fire the ignition or fuel injection. I bought $500 worth of HES's that I didn't need and spent untold hours troubleshooting due to a starter problem I had experienced before. My advice... pull your starter apart and inspect.