Right here is the most likely issue.
When you install mods for any game, those mods will leave data in your saved game files (and possibly installation) that references data that is included in the mods themselves. When you remove mods, you cannot remove the reference data that has already been recorded in your saved game files. There is no way for a save file to recognize that the data it's referring to is no longer there (as the mod files have now been removed). We call this stuff "
reference data". (Basically, instructions that don't lead anywhere, anymore.)
When a game is updated, files and data that mods refer to can and will change, meaning that the instructions the mods use will not be recognized correctly by the game any more. This can lead to all sorts of glitches or crashes.
Now, not every mod will change things in a way that will cause issues. But if a mod
does create an issue, there is no way to fix that except for the mod author to update the mod to work with the latest version of the game, according to the new data introduced by the official patches. This is how modding works for all games across the board.
When there are issues, they can be wild and crazy. Game elements don't connect together the way people might
think they do. It's possible for a mod that changes weapons to break the lighting system in some places. It's possible for a mod that introduces custom clothing to break an inventory menu. A mod meant to skip a logo screen might crash the game when you save. Players need to be aware of this, as these problems can and will occur on any game -- even if you've never seen or heard of it happening yourself.
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TL; DR
Best bet for your situation is to proceed with a
CLEAN installation and begin a new playthrough. The only other option you'll likely have is to reinstall all mods using versions that have been fully updated to work with whatever the latest version is at that time.
This may also help:
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