

That's not a massive issue since I can just re-install them from the downloads pane.
REINSTALL UPDATE ESM SKYRIM MODS
Long story short, I noticed that A LOT of my mods had disappeared from the left hand pane. No issue since that was just after character creation.
REINSTALL UPDATE ESM SKYRIM MOD
Glitched game, so I tried starting by continuing from the last save via mod organizer. Since I'm not completely immune to mistakes, I went ahead and manually browsed to the location to reinstall the path through mod organizer. It looked good, but still launched a glitched game through mod organizer. This made me think the path for SKSE may have gotten changed, so I checked that. First assumption was SKSE was messing up, so went to the SKSE launcher in the game folder, and launched from there. Went back to mod organizer, clicked on SKSE, and got the same glitch as before. Game worked fine, albeit without any of the mods. First assumption was Steam had updated, so I closed out mod organizer and launched from Steam. This morning, without making any changes, noticed that launching with SKSE started the game and got all animations, but the scene wasn't going anywhere.

Anyway, I had started the game probably 30 times via mod organizer using SKSE. I'd been doing test starts with the build after every 5-10 mods to make sure nothing was causing a CTD on start-up (had that problem early on and was a pain trying to figure out which mod was causing it). Finally got a working mod build after several days of downloading, cleaning files, deleting conflicting mods.
