Another update: We managed to fix most of the remaining bugs by entirely relocating the Colorizer code to bank 5. I managed to fit the code that calls the bank 5 code (and saves and restores the banks so interrupts still work) in about 20 bytes so we could fit it at the beginning of the ROM (the game doesn't use any RST lower than 28, so there are 0x28 free bytes available in bank 0. Most of the glitches caused by colorizer itself were because it overwrote a bunch of zero bytes later in bank 0, however these were important data for what happens when objects collide (eg. when you try to ride a boulder, or when you shoot a boss). A bunch of the glitches we caused when trying to relocate code were by not being careful enough about restoring the bank to the right place.
The one remaining glitch that I know of is that the timer now acts a bit glitchy - I think this is because there was an "ei" instruction in the timer interrupt handler, which we disabled because it was causing a lot of crashes, which funnily enough is because original code just assumes that any interrupts that occur WITHIN the timer interrupt won't change the bank. So perhaps the original code could be modified to fix this.
Anyway, I have one question for anyone familiar with GBcolorizer - is there any way to edit ROMs that have already been colorized and change the colors around? This page
has a lot of cool concept art, and IMO the color choices there look a lot better than the ones MathUser used in his hack (no offense).
Oh, and here's a screenshot of one bug that occured due to careless bank switching:
Edit: It looks like the only way to modify previous color data is if you have the .gbp file Colorizer makes. MathUser, do you still have this file/would you be kind enough to upload it for me?