Some updates:
* I believe I've fixed the pre-emptive Aps glitch. For future reference, I set the battle flags in Proud Clod for Aps, etc. to FFE9 (they were FFF9 before) which seems to have done the trick.
* I didn't mention it before, but the materia smuggle glitch! Apparently the null slot used in that glitch reads which materia slots are accessible from the Buster Sword and the Bronze Bangle respectively, which makes sense. Since I'm not using Cloud in this mod, I just removed the Buster Sword's materia slots and that made smuggling impossible. (As a funny aside, one thing I tried before deciding on that was the menu 17 "remove character's materia" on character 255, which removed all 16 MP Plus materias from the null slot. So much MP Plus!)
* Hit a bit of a snag with the snowboard minigame. I know that Tifa has a snowboarding model, but I haven't been able to call it for the non-Gold Saucer version of the minigame. It's possible her model isn't even loaded. Might need to see if I can replace Cloud's model with Tifa's or something.
EDIT: I've confirmed that Tifa's model isn't loaded, and there doesn't seem to be an easy way to put it in at the moment, so I've just skipped it for now.
Progress is going pretty good so far, though! The mod is currently playable through disc 1, and I just started working on disc 2. If anyone wants to test it out, let me know.