A few questions... Does it always happen between the same gears, or does it change? Is there any chance you are kicking the side stand down a bit when you shift occasionally? Could there be a short in the side stand switch? Saying it feels like an electrical stall makes me wonder if there is something shorting as you slow or clutch. Any chance the kill switch on the bar has issues? Those are just a few things that came to mind. You could bypass the side stand switch and see if that ends your problem, though make sure you don't take off with the stand down!
Hope you can find the issue. That sounds like no fun.
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