E. Borneman's response from his Marine Depot forum:
"Those look like extrusions of mesenterial or acontial filaments, not worms. Can you remove them from the coral without breaking them? If not, your coral is stressed by something and is extruding them through the coenosarc. Pretty common response."
Based on what I've seen so far and the discussion here, this is latest theory:
Stag - The Ca and Alk drop that started 3 weeks ago was gradual enough not so shock any corals but eventually caused this relatively fast growing stag's skeleton to start decalcifying and breaking apart . The loose shards of skeleton started to work their way through the coral tissue causing the rough appearance and tissue recession. Most of the affected areas were on vertical surfaces or the undersides of horizontal stalks. Handling frags and rolling them around in the microscope dish irritated them, causing the mesenterial filament defense response. All told, I probably spent a couple hours peering through the microscope. If there were any alien parasites, I would have seen them. The fact the the skeleton damage occurs before the tissue damage indicates it's probably not something coming in from the outside.
What's left of the stag in the isolation tank still looks good. I'll take a few photos tonight to compare to the initial ones. I'm pretty confident that it's not hosting a plague that requires quarantine from the rest of the system. Provided the chemistry in the main tank is back on track, it should have an easier time recovering in there than in the little 3 gallon it's in now so I'm planning on putting it back tonight.
ORA Yellow Fuzzy - This guy got beat up bad after the nose dives into the favia. I don't have any reason to suspect there is a parasite issue with this piece either. It's already back in the main system. The tissue recession on it hasn't progressed much if at all during the last week, so given good flow and low to moderate light I'm hoping it will recover. There are a couple small sections that have a more full greenish color to the tissue so I think it's heading the right direction. As long as a couple polyps make it through, it'll grow back.