So I closed out NMM and proceeded to nuke the 'Install Info' and 'Virtual Install' folders, reran NMM, and all the mods are now unchecked and light gray. So I RAR backed up the Skyrim folder in Steam and in /my documents/games, told Stream to uninstall Skyrim, deleted those two folders, told Steam to install Skyrim, ran TESVLauncher and configured Skyrim, dropped in the last SKSE files, ran NMM 0.72.3, and it showed all 98 mods still installed. It's been years and the little issues here and there and the crashes are were getting annoying.
I decided to reinstall Skyrim LE (Oldrim) from the ground up.
I get the feeling I'm going to get someone to thump their head against a table.