You used IMG tools then, I must say it was a bad idea not to backup your files. But if you re-install your whole game, the files will be back to normal
EDIT: I see that you edit your post with some more info. If you have v2 you won't be able to install mods without downgrade. If you talking about backups, a re-install will fix this problem. If you can find the backups somewhere you might try that first, google it, if not you should re-install the game.
Ehm...are you using v2, savefiles, after downgrading?