Using decompiled files: Acceptable.
Using the Source SDK's files: Great, at least with a little tweaking, as they're outdated.
Using a mix: Probably a bad idea.

Are you basing the QC and mesh files off the ones included with the Source SDK?

Actually, I guess you're right about it not being fully fixed. My hard-ware morph Team Fortress 2 Scout model gets shadows and rim-lights it's not supposed to when messing with the flexes. Even to an extent where a mouth flex will warp the normals around the eyes if a certain combination of flexes is used, even though the mouth flex does not modify anything besides the mouth, especially not the eyes.

Looks like a mip-map issue to me. As in, the biggest resolution is fine, but all smaller mip-maps of the textures are just black.

You are supposed to copy-paste its/their content(s) here.

I said material(s). You know, the material(s) of the model.

No.

That depends on what you put in the material(s).

Don't include "materials" in $CDMaterials, and probably don't have a slash at the start, either.

Then it only supports SMD, it seems. Oh, well. At least you made something that works for you.