I also have only a tenuous grip on electrical theory, but I think I would be much happier running a three phase reg/rec with a single phase alternator and not the other way round.
Those yellow wires melt when there is an increase in resistance and this often damages the rectifier. Is having the wire not connected, the ultimate resistance? The power from those alternator coils on that phase has got to go somewhere. Would it work better (or at all?) if you ran the spare wire from the alternator, to earth?
It all sounds like dodgy practice though. It would be a shame for your nice new reg/reg to arrive and then have a fried alternator and/or a fried reg/rec for the SS.
I feel your pain though. I know you want a ride on Sunday.
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