Alternate textures are skingroups. Some of the eye controllers don't respond until you save the scene and close/reopen SFM.
I highly recommend *not* dumping this into usermod, you should create or link this as a separate mod that usermod can reference in gameinfo.txt. That's how the release is structured and what I stated as its preferred use in the description.
The SFM loading screen does make sense, and it probably replaced the default usermod gameinfo.txt as well, which is causing the missing links. You can generate a new gameinfo by creating a new mod and copying its gameinfo.txt back into usermod and replacing any instances of your mod's name with 'usermod', although there may be a better way to do this I'm not aware of.
It's going to be a project to undo the damage if you don't have a backup, sorry for the inconvenience.
Well it's not dead per-say, just long done. It just never saw a public full release.
Man, I just extracted these files for a proper port. C'est la vie!