Okay so I used console commands to give my self some gear, boost my archery, give lydia better armor. I took a sword from her and walked outside. All the guards.... NAKED. I would like to fix this and I really dont want to redo all the stuff I did between then and now....

Just go back inside your house, and reload the game, or load a previous save. Using console commands is not recommanded, unless you have no choice.

I doubt it has to do with console commands. It seems something that originates out of not loading properly some in game assets.

If the issue persists also when loading an old savegame (which, I hope, you were diligent enough to keep) try reinstalling the game. It could be well a corruption issue of the main data file.