My old Honda motorcycle would not run on one cylinder so your engine is a mystery running good on one.
Does this engine fire both plugs at the same time or one at a time? Mine (different 2 stroke though) fires both at the same time because, both pistons hit tdc at the same time.
I have a couple guesses, one that your stator voltage is to low and it will not fire both coils or that your plug gap is to large. Also look at the clearence between the flywheel and the coil pickup, if this motor has one?
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