It was just a couple of files.
Now there's a new and interesting twist. NMM is just slow, period. I'm having a problem with skyrim that I haven't been able to solve, so I decided to just rebuild it all again to try to track down the proble. So with that, I chose uninstall all active mods. It's been chugging for about 10 hours, and has made it through about 20 of the almost 300 active mods that need to be uninstalled. At this rate, I might get to start my rebuild around christmas.