After a long run of modding, I decided I disliked my ENB. I removed the files, I started Skyrim, it crashed. That's fine, it's happened a thousand times before. I go into my Skyrim folder and delete the folder, then go into My Games and delete the Skyrim content there. I go into Steam and uninstall. When I reinstall, my game is broken. I click start from the splash screen, and it blinks, returning me to the splash screen. Eventually, I got it to play, but it is in a permanent windowed mode that I cannot change, even in the .ini files. Please help, I really miss this game. I'm 80 hours in and haven't even touched the DLC's yet. Has anybody faced this problem before?

It almost sounds like you did Marks uninstall method.

The last part would be to run CCleaner

I would maybe also check you video card control panel or if it has program running in the background. Some might have settings based on users playing the game and it is quite common for people to use windowed mode in Bethesda's Games since full screen mode is quite a bit flaky for Alt-Tab and some people get better performance in windowed mode.