This is what happens after the FOMOD installation:
http://img294.imageshack.us/img294/6774/screenshot11q.png

Anyone know what's wrong?

Better lose that link, nvde stuff isn't allowed here. But it seems textures aren't where they should, or you haven't applied archive invalidation.

Bits are covered, it's fine.

I used to only get that with Raiders. I don't remember how it got fixed.
Usually I open meshes in Nifskope and see where their textures are pointing to, hopefully to the right ones and if not I redirect them. Other than that I don't know. I created my own fomod so I was sure everything was in the right places as some people can't pack an archive correctly.

nvde parts are covered. Anyways, does anyone have a better solution?

You've copied the meshes, but not the textures.