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One of the sporty guys had this problem, as did I. It can be one of two things, coil or ignition module. The way I tested the coil is swapped the module wires on the coil along with the plug wires. Essential single fire coils are two coils in one. By swapping the wires around you are switching coils. If the bike continues to run on the same cylinder then the coil is bad, but if it switches cylinders then the module is bad. My problem happened to be the module so I changed it. I don't see how the charging system could cause this problem due to the fact people kill batteries all the time and it never hurts the ignition. Ignition general needs 9-10 volts DC to work. Hope this helps.
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