Okay, mini-bump.
I've gotten the models to sorta work. I can even get the textures to show up in PCS and stuff, it's just that in FRED the model doesn't show up at all. I can't remember if I tried -jpgtga or anything like that at all, but I will. Anyway the issue with the killed meshes and stuff is fine, it's just that some of the faces don't show up, even when I know their correct. I'll look into that more later, and hopefully my texturer knows how to make this stuff work.
I'm probably gonna be finishing up with the story next week, assuming TAP doesn't flood me with stuff to do. Once I'm done with that, I might want one or two people to look it over and try and find plotholes and stuff. So I'm opening another position for "storyline proofreader".