I know it's two in the morning local, and I'm just tired and frustrated... but I can't help but seriously consider shit-cannning the entire NCCS project again.
Ran the game again finally. One companion still locked up. Ran the game several more times. Same companion locks up every time; right after combat ends the first time. She'll still follow, still respond to threats; but once combat ends the weapon gets put away regardless of whether mine's out, and she won't sneak under any circumstances.
I decide that perhaps the new companion script is getting too hefty for the engine to handle; cut out some code from the affected companion's script (but not the other two, to keep a control). No change.
Load my old "clean" save in Doc Mitchell's during character creation. Get through that, get out into the open... and now no companions work. I can't talk to any NCCS companion, and they can't talk to me. I have no idea why.
So, at this point I get to begin the process of clean saving, new games, and pacts with forces of Darkness to try and figure out what in the holy fucking everloving hell is wrong with this goddamned game this time.
Mod for NV, I said. You'll be able to get in at the ground floor, instead of a year after the fact, I said. It'll be the next CM, I said...