The fastest way I found to get FFXIV running in a new OS install is back up the game folder at C:\Program Files(x86)\SquareEnix\Final Fantasy XIV as well as the game settings folder found in documents/my games. Then install the FFXIV installer but don't download the game. Basically want to get it set up to the point where the game will start to download, this takes care of any system registry stuff. Then you can just copy over your updated version with overwriting any files then it will work fine without having to re download everything. Also put your settings back in the my documents/my games folder