1) You could have problems with the engine kill switch on the right bar.
2) You could have wiring problems.
You stated that when the engine problem occurs, the ECU initializes and fuel pump primes as if the ignition was switched off and then on.
I'd also check the wiring harness on the left side, under the fuel tank.
Where the harness passes over the rear frame section, it's very near the bottom seam of the fuel tank.
It's very easy to pinch wiring at that area, causing momentary opens, which it seams you're having.
Not an easy thing to troubleshoot. But it's happened in the past.
I know when I was working on mine back in '08 I noticed this, and took quite a bit of time to try and route and secure the harness to prevent this.
Even now, if I raise that tank, I SLOWLY lower it and visually check all's clear.
Last edited by SubSailor; 08-03-2012 at 12:27 PM.