One word... structure. Where is it? Put everything you have in patch form and it'll be great.
By the way "patch form" mimics the file structure of the mod's existing textures starting with "assets" or "mods" depending on the version of Minecraft used for the mod; mc1.6 uses "assets". Also, don't include any default textures in the patch, please; makes it easier to batch resize.
It's gonna be time consuming to fix it. Take your time tho.
I'll try working on it myself for ideas.
IDEA: I've started mashing the whole list of Sphaxified textures through each of the mod's extracted assets folders on a "keep both but rename" pattern. The textures to separate have some kind of renaming convention such as adding " (2)" to the end before the extension. Try using that to split completed textures off. Also, I've found that the mudoraBg and dummy textures appear in two places; the dartcraft folder and items folder. I don't know for sure if the ones in dartcraft are unused or not, so I'm leaving duplicates; even though I think the mudoraBg in dartcraft is actually supposed to be a gui of a sort. Strange file structure. @_@