I didn't read the whole post, but I had a similar issue just before the warranty ran out.
My 2009 R3 would cut out momentarily while in motion and, at other times, not cycle up when I turned on the ignition - with the kill switch in Run.
It turned out to be a connector in the circuit powering a relay that cycles up the ignition system. The tech by-passed the offending (burned and corroded) connector and all has been well for the last year.
