I swear, I'm never going to get out from under this goddamned mod. No more am I joining any teams, or "inheriting" any mods. Ever. Any frustrating failures I have to deal with will be my own. I make enough mistakes on my own, thank you very much.
In any event, someone took up the hobby of deconstructing RR in FO3Edit, and pointed out some shit to me that survived my seventeen other purges. For some reason, there were modifications to idle markers, position of an item in Moira's shop, and there was an old part of the prisoner system that was flagged as renaming the Alienbeaconradioscript. Not sure how they escaped my notice before, but all such overrides are fixed now, leaving only the modifications (door placements and such) that are supposed to be there.
I should have went with my first instinct a year ago, and trashed the entire plugin; started anew. Would have saved me weeks of trouble, on the whole.
Oh, and link.