You stator output is an AC voltage that is rectified by the regulator turning it into a DC voltage to charge the battery. I am not familiar with the later model bikes with the Twin Cam engines. However. if there are only two wires in the plug that plugs to the stator, it does not make any difference which wire goes where into the plug. The only wire that does make a difference is the wire that goes to the battery with is the DC output of the regulator. Usually that wire is a larger diameter wire due to the larger gauge wire and heavier insulation on it.
Good Luck
Steve
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