Sadly, this has caused what I feared most... I've started hacking and tweaking things I have no business doing.
First off, got the Woolsey's Uncensored patch working for FF3, seems it was a header problem. On that note, I got Chrono Trigger+ to boot, but it seems I can't get out of the bedroom. I also tried a Chrono Trigger retranslation, but it freezes on "chrono" when waking up. Not sure if they are touching anything relatively vital, or if it's the fact these games are outside the normal hi-rom range (48mbit, but most games tapped out at 32mbit) and the emulator doesn't support it.
I also have a hunch or two on what's causing Illusion of Gaia/Time to not work... going to prod it a few times and see if I get anywhere. Honestly though, it means delving into the SNES arch and ASM on a system I'm not too familiar with, so it'll take a few days before I know if it's something I can do. That said, I'm fairly hopeful as I have a few leads based on looking at some emulator changelogs and seeing what tweaks they had to make to get the game running.
There is no special hardware in IoG, so Canoe should work with it in theory after we figure out what's causing the initial hang (I do note a lack of Sound in the opening, which is also hopefully a useful clue).