There is no problem.
When you uninstall, it copies the uninstalled changes to gas/changes. You have to manually move them back (the readme talks about how the changes take place). If you downloaded the backups - just replace your current files with those as long as you havent installed any other hacks since then.
It has gone crazy because you are running hacked files, but uninstalled all other aspect. In essence, its only partially uninstalled. Sorry if that was unclear in the readme (its pretty detailed).
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