Slight update, I've figured some of it out. This is what I see now. No idea what needs to be changed. I have all 3 body parts in there (and coloured white) and the windows. Still have a few issues, and the headlights are fully covered.
Here's a link since the pictures are gigantic and didn't resize.
https://i.imgur.com/z7Ls22N.png
Here's my saving process: flatten the image, export as dds with BC3 / DXT5 and generate mipmaps, combine it all into a mas file, put the mas file in the DIR folder.