Well, I don't really understand what's going on. I have the exact same files, and also my manual region fixes which are effectively the same as Solarius', the MiB race is well defined there, and I can take your "UAC Moon Keeps spawning.sav", wait until the moon mission spawns and get black Sectopods on the Moon and everything.
Did you try just installing the Github version to some other location, pasting your save over and seeing what happens then?