Update time!
I drained the pool down about a foot below the skimmer (I've read that much more than that isn't safe in fiberglass) and refilled it, keeping the chlorine high. It brought the CYA down a little, but not much. In any event, I think the algae is dead at this point. The water is really clear, but there's still a greenish cast to it. Problem is, I can't tell if that's a result of the staining, or metals in the water, or if I've still got algae and don't know it. Also of interest, I tossed a small bit of ascorbic acid, maybe 1/5 a cup, into one end just to show my girlfriend that the stain removes easily. That was days ago, and it hasn't returned despite the very high chlorine level. Not sure what to make of that.
I think I'm at a point where I can start letting the chlorine drop down to fight the stain. It's around 18 ppm now, and I'm planning to let it drop today and tomorrow and see what happens. If the water starts to cloud up again, I assume I've still got algae problems. Otherwise, I assume that the greenish cast is from the metals present. After all, the water shouldn't be CLEAR and green if it's algae right?