Do one thing at a time. Do not worry about the MODS, just concentrate on the list I gave you. Loading fresh vbulletin files, is a good idea. Disable your modifications/plugin system via "config.php" and make sure your master style templates are unaltered from the original (Use tools.php). Leave your modifications alone at this point. We are trying to create a known state, do not add more variables. Do not delete files, just overwrite them. Deleting the wrong file can complicate your recovery.
Little steps here with a backup between each step is advised.