How can I make Nexus Mods work. I can't get any of them to work in game.

Well, if you have reinstalled the game, just remove all mods and add them again in Vortex.
Make a game synchro (check files option) before appling mods.
If you don't use Vortex get it from Nexus. Saves a lot of clickin.

I don't use Vortex and have a few mods installed. All I had to do was create a subfolder called Mods and drop the extracted folders into there and they worked.