I've had similar problems twice in ~100,000 miles on a 2007 KLR. Once involved the kickstand kill switch, in response to which I jumpered around it so that instead I occasionally take off riding with the kickstand down (not recommended).
The other time was more puzzling, and turned out to be a detached baffle inside the muffler--sometimes this had no effect and the bike worked fine, at other times it merely choked off power above a certain speed, while on rare occasions it stopped the engine entirely without warning. Following lots of carb maintenance, wiring and fuel delivery checks, and other such stuff, I finally heard an audible "clunk" from the muffler while under way at the precise moment that I lost power.
Intermittent failures are ridiculously frustrating, especially in 2008+ models which rely increasingly on electronics. Sometimes, as with my defective muffler, solutions require sidestepping normal tunnel vision--in my case, I was absolutely certain I was dealing with a fuel delivery or electrical problem based on the symptoms.
Hope that's helpful, and good luck!
Mark
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