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Next time it is running on one cylinder, and you'll know it because it'll take full throttle just to maintain speed, pull over and blip the throttle to keep it from stalling. Stick your hands in through the fairing openings and wiggle the coil connectors. If that changes the way the engine runs then you have problems, either corrosion in the terminals (they're not water proof in the least) or the wires are broken where they're crimped into the terminals. I had this problem last year, it took forever to track it down.
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