The cid thing sounds like a logic flaw of some kind, maybe to get around some problem or other. I'll make a note to check that out.
The Da Chao fire cave event triggers when the 2nd chest is opened (or it may have been when the last set of fire is cleared out) so updating to the new version after clearing out the fire/chests will probably have ticked the activation variables, rendering it unavailable. If you missed the battle, then you could try downgrading to 1.4 again and checking out the shrine in Godo's House, the fight used to be found there instead.
Sandworms should be behaving themselves in the 1.5 version, as for Hellmasker I don't know, maybe the Frog status from his Nightmare attack if you're using 60fps mod or similar; seems that status breaks it.
As far as cid and the final dungeon goes i noticed that he doesnt attempt to jump down the first few steps (like cloud does) so maybe it involves cid's jumping animation.
the hellmasker glitch happened when i used the limit. Vincent just stayed vincent and didnt even transform causing the game to halt. i was on 1.4 then i think though so it may not happen in 1.5.
Either way thanks for the awesome mod! gonna replay it again with a different team comp