So I followed the Vanilla guide, I noticed i'm missing the "reslists" folder, but all other folders are intact. DirectX10 folder doesn't have 146 listed, but 196. All other folders had what was required already and didn't need any additional deletions. My Documents/Games/Skyrim did have a few files in it about SKSE and a loader, so I backed up my save games, deleted all files and tried to start the game. I didn't put back my save game before starting. The game still crashed. So outside of the few things I pointed out, I'm not sure what is going on. Verifying the integrity of the game, it is always missing 1 single file. I've googled this and apparently it is very common and isn't necessary to play.