Short update:
So my five surviving dwarfs are all doing well, everyone seems fine (up to 79 pop now, thanks to heavy migration within the first year of rebuilding), but I did have another disease scare. Two animals got the same foot rot as the batch who died during the apocalypse, they were giving off miasma and basically I was convinced I was about to have another severe population collapse. Both animals died within the year, nobody raged, and a year later, there's still no dwarfs with any incurable infections. So.. "whew."
The fortress has another FB in cavern layer 2, but I'm keeping all the cave systems locked down for now. I have no immediate reason to go poking around down there since my exploratory expeditions didn't yield any visible cotton candy spires or anything.
But this fort has a much more serious issue at this point. I created my first ever waterworks. It's really great, the design is a very simple, single stack of pumps that draws water up from a brook to the desired terminal Z, pushes it underground and then back up to a fountain & pond in my meeting hall/well room/statue garden, which itself drains into the brook at the top NW corner of the map using side-by-side pipes for intake/outlet. It's actually really simple and cool looking, and provides a constant source of mist for my dwarves to revel in. Many of them are well over 1000 happiness now.
The problem now should be obvious. FPS death. I'm running at ~38 FPS right now. It takes many REAL minutes to get anything done in my fort. Even simple stuff like cage trap assembly, construction demolition, etc... It's ridiculous. I can't go back and "undiscover" the caverns, I've used or otherwise eliminated pretty much every piece of non-economic stone on the map, and shutting off the waterworks doesn't stop the flow calculations rapidly enough to be useful, so anything I can do isn't going to bring me any great FPS benefits. I'll play it for another couple years, make a backup, and abandon it so I can check it out in adventure and legends modes. I can't believe how easy it was for me to pull this fortress back from the brink of utter annihilation (not to mention how easy it was to almost utterly annihilate it), and it makes me sad that now that it's barely started its second life, I'll have to abandon it.