For a completely clean, unmodden version of skyrim I'm pretty sure all of the meshes and textures should be in BSAs. Meaning there should not be a Meshes or Texture folder in the Data folder. If there is, it's overriding the BSAs.
The thing about textures and meshes is they can look ok, but still not be in the correct format for SSE. I've run into Oldrim textures that will crash SSE. Oldrim meshes need to be optimized.
You could give this a try. https://www.nexusmod.../4697?tab=files It will clean up any leftover files after you uninstall all your mods.
It's looking to me like you may need to start over with a clean install and add mods back in One At A Time until you find the culprit.
At the very least drag the meshes and textures folders to the desktop, Or rename them so they don't override any BSAs. Then fire the game up and see if you still have an issue. Missing textures and meshes shouldn't crash the game, but you may see "purple" textures or red squares with "!" in them. But, if your install is clean then those things shouldn't happen.
I'm not trying to funny here, or anything. I'm just not sure what all you know about modding Skyrim. But, make sure none of the mods you are trying to use are for Oldrim.
What mod manager are you using?
Edited by TheWilloughbian, 18 February 2018 - 06:03 AM.