I really need a tutorial on how to fix this, because well M22K, you probably already have seen how my Melee Fox looks like right now and it's messy in regards to his shader.
To be honest with you, that Fox you're talking about looks lots better than what Melee Mewtwo looked like at the beginning. From what I can see, there are only a few problems in the arm and fingers, nothing more. Mewtwo was completely inverted.
No tutorial needed, what I did to Bowser and Mewtwo was exporting them as .dae (cause I didn't have the original files used), open them in 3dsmax (normals get reseted) and, the basic edits I guess every model needs is, using the 'normal edit' modifier, rotate the normals in the right arm and leg (the left ones seen from the front) 180º in X. The will get dark in 3ds and brawlbox. If you look at the original character models, this happens with most of the character if not every of them. The leg and shoulder bones are rotated 180º in that side, and that's the reason the normals are inverted ingame.
Aside of that, there are those glitches related to rigging. I can only think of editing the normal for each vertex to fix those.
I'm gonna take a look at what can I do for your Fox now.