I just took a look at my backup .iff file in the Mod Tool and noticed that on default, Stern's arm skin looks like this:

I'm wondering if this might be why his arm's and face looked like that when I tried to import Scalabrine's texture over his. I replaced 0 on that picture and literally nothing changed. The arms were still black, but Stern's face and arms weren't glitched like before. As soon as I replaced 1, the glitch happened again and his whole arm was covered in those weird pixels.
Also, Stern has two extra file slots on his file that Scalabrine didn't and they look like this:

I tried exporting over these too, but all it did was leave his face normal except for a few random pixels around his face. Am I doing something wrong or is Stern's file different from other player files?