In the pictures you can clearly see that there are marks on both the stator and the magnets; they have been rubbing together.
From the info we have now, that looks to me the cause of the damage; what happened next? Hard to tell. Perhaps two of the coils (in different phases) got into short-circuit (shorting both phases together) when the wires were bare and a magnet passed, shorting both together.
The repair? A new stator at least.
Depending on your own preference, perhaps new rotors too. Though this one might be salvaged (re-painting/protecting the magnets) don't underestimate the harsh weather environment. Personally, I'd take it to be an (expensive) lesson and make new rotors.
To prevent it happening again: make sure your bearings are ok, and that your airgap isn't too small. I'd rather have a few % less power than a same incident again.
Too bad. The alternator looks very nice, rotors and stators were built very nicely.
Nature and mechanics can be very unforgiving for errors we might consider to be minor, or details.
Peter,
The Netherlands.