I am not good at this side of things. Something looks horribly wrong, as it some of the apps are messed up.
The first thing to do is to back up all the backup snapshots in /var/clearos/configuration_backup to a PC or somewhere so you can preserve the earlier ones. I would then try restoring an older one. I have a feeling this won't help due to your errors and perhaps some of the apps may need reinstalling.
Have you at any point had a disk crash or run out of space on the disk?