So I tried to open up MGEXE.gui and it keeps telling me it can't find the Morrowind Registry files, and to run the game as an administrator before installing MGEXE.

I am running Windows 8, and this never happened before. I tried uninstalling MGE and reinstalling, didn't work.

I installed it to SteamApps>Common>Morrowind. NOT under Program Files (x86)

I think SteamApps needs to be in the second position in the path. Like Steam/SteamApps,