Ah found my issue, I was extracting the files to an old folder for FFXI that's on my computer for some reason when I should have been extracting them to FFXI in my steam folder, "Version update complete."
Anyway seriously anyone still doing this the normal way go to
this site and extract the files to your SquareEnix folder and then run the update, it will save a lot of time, I only had 2 files to download.