This doesn't look like an overload burn out, either something has caused shorted turns ( loss of load in high wind and excess volts?)  or your magnets have rubbed the stator and caused shorted turns. This has happened but I can't tell whether it is cause or effect.

Others may think otherwise but I think you will have to change the damaged magnets sooner or later. If you stop the corrosion I should be surprised.  Difficult to say from pictures but your coils don't seem to have a lot of wire and the holes look bigger than the magnets. Dismantle the remaining coils and see if they are cooked inside, maybe they are also on the point of burn out even though they look ok.

The wiring in this case seems to be Star, so the common point is star connection and the short occurs at bottom of phase 3 and second ( middle) coil of phase one.

If I were going to build a cast coil set up, I, FOR SURE, ALWAYS, will bring all phases wires externally, to allow proper testing and wiring once the Stator is cast and set.

Regards

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.