I´d check the wiring coming in from the timing advance unit on the right side of the bike. Where it connects to the harness in front of the battery on the passenger side is a white connector. If this connector is loose it will cause a the bike to misfire on one bank or the other sometimes alternating. This drove me nuts until I figured it out, cut the connector off and solder the wires together. If this is your problem you can test it by wiggling the connector or removing the spark plug boots systematically to see which ones don´t effect the running of the engine. Also, take the cover off of your timing advance on the right side of the engine and lube the hinges on the advance unit. Hope this helps.
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