When the bike seems to lose power, pull over and carefully touch the exhaust downpipe from each of the cylinders - if one is cooler than the other then you can determine which is not firing. If all ok then i'd look toward the coils, and if no problem there then check the air-intake for the field-mice/hamsters/gerbils etc  (i once had an intermittent blockage here with a rag in the airbox intake, so it certainly does happen...).
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