If you still have 3 wires coming out of the loom it suggests the 12 volt conversion hasn't been done properly. The 3 wire system switched 2 of the alternator coils into circuit when the lights are switched on.
The 12 volt system is much simpler - 2 wires from the alternator to the reg/rec then 2 wires out - one to the battery, the other to earth. It looks as though you'll have to investigate a little further.
If you have a 3 wire alternator you common the light green and dark green then use this as one input to the reg / rec, the other being the white.