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Dave, it's been a while since i worked at alternators etc and i've never worked at ducati ones but, i think your 3 wire alternator is three phase. The 2 wire rectifier will be for a single phase one which the older ducatis were. You would get voltage ok but you wouldn't be drawing from all three coils of your stator in a balanced way which could possibly damage it under load.
Anyone, please feel free to correct me on this, i'm rusty on this stuff nowadays.
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