What worked for me was going to the article someone else had already mentioned, but keying on this piece:
application.config.backup is not created by automatic backup. The backup files are in %systemdrive%\inetpub\history directory. Automatic backup is also a Vista SP1 and above feature. More information can be found in this blog post, http://blogs.iis.net/bills/archive/2008/03/24/how-to-backup-restore-iis7-configuration.aspx
I was able to find backups of my settings from when I had first installed IIS, and just copy and replace the files in the inetsrv\config directory.