Back up game saves.
Uninstall game.
Delete the entire game folder. <the only way to be sure you have removed any mod changes>
Reinstall game and verify function in a new game with a new character.
Add mods in one at a time to see what mod is causing issues.

This is not to say that the game won't change over time, I think they are experimenting with ways to optimize the graphics. But the only way to be sure your issue is really the game is to do the above.

If you find a mod that is causing an issue then report it to the modder.
If you feel the game is still an issue, and you can't compensate with settings, then submit a bug report in the proper sub forum.