All right, I've got this mostly figured out, but one aspect of it derails my progress. You see, with 3DS textures, there's a common error when they are not converted properly. The specular maps become the alpha of the full image, and if they are not extracted properly, removing them will result in just a completely black area anywhere the alpha masked. Now, I have a method of converting these images, however it is not able to do them properly, resulting in the error I just described. I was hoping someone would be able to find a way to convert these, separate the specular "alphas" from the image, and retain the full colors needed in the diffuse textures.
For those of you who know 3DS format compression, they are usually either ETC1 or ETC1A4 encrypted. I have included the makeshift progrram I use to extract them for now, but as I said it does not do it properly.https://www.dropbox.com/s/u1hoa9ruz85i4gq/Beerusis.zip?dl=0