Well, I thought I had a problem, but it turns out that the game must have just freaked out for some reason. I quit, went back to an older save file, and what I was experiencing is totally different than what I was trying to make sense of before. So, nothing to report, I guess.
I really like this mod. I like seeing the background of Shadow, the conflicting ideologies. It's very well thought out.
I'm going to go back to playing, and then I'll come back and tell you my overall impression of it. As of now, it's very good. Oh, and I'm up to the part where Shadow's been knocked out in the mining caves, playing at being the Sith survivor.