So the same issue persists even if the carbs are switched, and once running, there are no other issues? That's a good one... If it's not a traditional air leak, here are my shots in the dark:
• Is the kickstarter gear lined up correctly? I'm talking about that one that drives the gear on the crank; I've had that slip out of alignment before so that the part without teeth rotated to the part that should have them. But it felt wrong when kicking, so you'd probably have fixed it already if that was it.
• Rings shot? A little pressure could be creeping by, which might not be as noticeable when riding.
• And it fires on every stroke? Like, the CDIs not crapping out every few charges with a weak pulse?
I've have this happen, but it's always kick-start-assembly related. You talk to the pro about this one?