Meh, this has been on my list of things to do. The main problem is finding the location of all the changed textures, there are actually a ton of textures in the game that use the new Gerudo logo (crystal switches, floor switches, a wall in the forest temple, mirror shield, blocks, Ganondorf's cape, several in the spirit temple, to name a few). It seems they also ran a script against the game's source code and automated changing any references from blue to green, and green to red. As a result you can find some pretty strange changes, for example the fairies in Kokiri Forest are the wrong colors. The gamecube release also played a video for the ending credits instead of the in-game rendering the n64 version had, so this needs to be re-enabled in the rom as well.
OoT might be more of a headache for editing text, just because it requires extra bytes for coloring the controller icon characters (MM had ASM that assigned a default color, which was more of a pain to find but gave you more room to work with) and they changed several references from "press" to "tilt". If it's anything like MM, text has to be aligned to the nearest 4th byte (ie. 0x0, 0x4, 0x8, 0xC), which means you may have to change hundreds of offsets to add a few bytes to a string. No tools exist that I know of to do this automatically.
I've already done the GC MM USA rom (also has the PAL script/sound changes) with corrected n64 colors if you're interested. http://www.mediafire.com/download/s4k2kte3r2k07uv/MMgc-n64.zip
For the GC MM PAL rom I've only really done the n64 colors and haven't done much with the text http://www.mediafire.com/download/il54bl873k8emsg/MM+gc+pal+n64d.zip
Use Floating IPS
to apply the patch to the untouched Big Endian (.z64) roms.