Other than restoration from a backup, there isn't really a method to restore your configuration, or wrappers configuration (styles), or custom islands from being overwritten.
What all did you replace? The only thing that should really matter is that your includes directory is complete as it includes information for scripts to communicate with the database.
Are you attempting to perform an upgrade to a new version or to one you're already running? The upgrade utility assumes that you are upgrading a fully functioning forum.
Files displayed in the management screen in the upgrade utility can be found in the install folder, I believe it's upgrade_changes.txt, simply remove the offending lines between your target version and existing (the lines have version indications).
UBB.threads is only a few megabytes if you only backup operational files, I'm sure you have enough space for it to be included in your backup plan.