Got 4-bit textures hooked up. Still need to fix palettes. Interesting to see that things are laid out a little differently in the PC version.
EDIT 9/22/11:(palettes are now working)
Been a while since I've done any work on MGS. I've got VRAM partially simulated now. 4-bit textures are incorrect and palettes are totally broken but its better than nothing.
So I decided I don't like using Noesis for Ninja format stuff so I'm writing my own loader from SANiK's notes. This way I can add support for Ninja Texture Lists(NJTL) and properly support GBIX IDs and PVPL palette swapping. Noesis also seems to ignore the translation data and you end up with a hot mess if you import a group of models. It also seems to have iffy UV coordinates.