I probably converted GIMs differently to you. from what I can remember, I used two different versions of a program called GimConv.
1. Get original dissidia texture and edit it as you see fit
2. Convert to 'SGIM' (Just a name I gave to GIM v.2) using a later version of GimConv, the one that handles BMP>'GIM' (Really it's SGIM, it won't work as a dissidia GIM)
3. Get the early version of GimConv which can only handle TGA>GIM, but instead of TGA conversion, just use it to convert from one of the types of GIM to another (i.e SGIM>GIM). This should leave you with the original BMP texture in regular GIM format. I used some weird program called 'Puyotools' or something - which wasn't designed for dissidia at all - to view the resulting GIM files. they looked OK here, apart from the buster sword, which seemed to lose colour down the handle.
4. Insert back into model file with hex editor then recompress ISO
Oh and thanks, I also gave him "Crisis Core" style clothes (i.e I stole some textures for his face, top and armour and recoloured bits and pieces like hair and clothes). They did go a little bit weird though, but again probably because I actually changed the face textures for the CC ones, as well as the animation GIM for the face. I spent ages getting the pixels exactly right D:
EDIT: Just realised I still have the programs I used on my PC, just ask if you'd like anything