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There are a lot of possibilities. Simple things to check would be the low tension leads on all three coils, and that all spark plug leads are on correctly. You could also check the Primary TPS, and the throttle body balance, and the crank position sensor. As the bike has very low mileage, I would also check all the fluids, and drain the gas tank and put fresh fuel in it. While doing that you could check the fuel filter to see if it is gunked up with bad gas. If it is then the injectors may be as well.
Has the engine thrown any CEL codes?
It could also be the wiring on the ignition switch getting ready to fail. If you don't have an Eastern Beaver kit, or something similar, then the ignition switch will fail at some point. It can be repaired, but you will still need the EB kit.
If you don't have TuneECU, then you should get it. It will help with diagnostics and settings.