Sounds like you've gone from the series-star wiring to the series-jerry wiring.
Like this:
(going from top-left (series-star) to bottom left (series-jerry))
Except in your case, you don't have the pairs of coils together, either. Now you have split each pair, too, and rectified them individually, too.
Confirm for me that, if the diagram does indeed apply to your case, that you have a rectifier across points 1-4, 2-5, 3-6, 7-10, 8-11, 9-12?
To me you have effectively cut the output voltage (per rpm) by 1/4, as your measurements confirm.
And if you picked any one of the leads coming out of series-jerry, plugged it into one of the ~ terminals of a square rectifier block, yes, it wouldn't matter which one it was.
The alternator could still be suitable for a WT, but that would depend on how its speed (about 250 rpm 12v cut-in) matches up with the size and TSR of the blades.
Moreover, this configuration of alternator has much much less resistance now.