Great to see your progress here, hopefully this game's code ends up as well-documented as the rest of it. Just a question, will this be a compilable disassembly, or just a reference, like the ones we have for FF6? I'm guessing the latter, given the amount of work involved for the former (I tried to make a compilable 01 bank...didn't get very far). I don't think I can provide much help, about the only thing I've looked into at all is the main menu, and that was only what printed the text, nothing else of the menus.
Speaking of the 01 bank, FF4's is completely compatible with every other version (you can drop the entire bank in, and the game will play perfectly), so it might be a good idea to disassemble that one instead of/in addition to FF2us's. That way the extra menus are all documented as well.