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I just had that same problem. I had the Dwemer Armory mod active and had tons of stuff in it. Gear, potions, ingredients (thousands of them), weapons, etc. I deleted the mod and everything went back to normal. In the process of deleting the mod i deleted all my stuff in the Dwemer Armory. I was...
Found out what it was. Dwarven armory mod, where i had everything imaginable stored. Got rid of that and now my load times are still long...but at least i can quicksave normally now, which was my major problem. Guess i was just hoarding too much stuff. Lost all my stuff when i deleted mod :(...
I unsubscribed to all the mods from steam, and deleted the one's from nexus mod manager. Then checked the steamapps\common\skyrim\data folder where all the apps seem to be stored to make sure they were really deleted.
Verifying it found a bad file but didn't help anything. However in my saves under C:\Users\Username\My Documents\My Games\Skyrim\Saves it says there are saves such as autosave1.ess and autosave1.ess.bak which i would guess stands for backup? Could that be the problem?
My game has run just fine on a complete quest completion once already. Decided to run again with a bunch of mods and i've noticed that my save times are around 2mins as well as my load screens. Even quicksaving takes 2 mins. Since i've already beat all the quests that i cared to once already...