I inactivated all my nexus mods and deleted them (wrote the ones I had installed down)

Im unsubscribed/deleted the workshop stuff.

Removed anything I put into the skyrim directory

What can I do to go back to vanilla in case there may be some things lingering around

Just delete the textures and meshes folder in \Skyrim\Data

its that simple?

And the non-vanilla BSAs and ESPs, if any remain. Then validate the files just to make sure it's all there.

I dont see a textures or meshes folder

just textures and meshes .bsa

Then you don't have any texture mods installed unless they came in esp format.