I managed to get the files back, had to specify the new path to the mv and cp command to get the command to work.  I'm lucky the execute permissions were still intact. Linux permissions are fucked like that, when you move files around they may or may not change. 
Managed to put everything back, but I'm nervous about rebooting as I can almost guarantee not all the permissions match properly now, and it may be an issue as some files may not be accessible or what not.