An update on Pirate:
The hole appears to have started healing. It's not red and raw-looking any more - instead it looks pinkish and like it's getting filled in.
However - she has started to bloat and pinecone, mostly on her right side (the opposite side of the hole). Her body is curving slightly to the left because of this, too. For a few days now, she hasn't been using her left side much (I believe I mentioned this in the original post), although she occasionally uses her 'flipper' fin.
She originally seemed to have trouble keeping her tail up, then she had trouble keeping her tail down for a couple days, and now it looks like she may be back to nose up. It's not a large angle - she's at about a 45* (or smaller) tilt, on average (doesn't go above that).
I started treating her with Maracyn on Monday (today is day 4 of the 5 day treatment) to help prevent the hole from getting infected and to deal with any other problems she may have, since I suspected something else going on, but it doesn't seem to have done anything for the bloat, since it has gotten worse since that started.
To my knowledge, she has not eaten. I've seen her knock flakes down from the surface when I put them in, but I haven't seen her eat any of them so far. The last time she ate was about Saturday, I think. No clamped fins, no bottom-sitting (she swims slowly, but pretty constantly). Gills pumping more than they should, but she doesn't look distressed about it.
I'll try to get some pictures of her puffy self, but my camera's brand new batteries apparently died (ugh!) and I'm out of double A's, so I'm stuck with my camera phone for now, and it's not great.