Missing Utilities after installing SSD and restoring from Time Machine

Today I installed an SSD onto my mid-2012 13" MBP (running Mavericks) and then ran the restore from Time Machine function to bring back everything I was using. All went well, except now I have discovered that Time Machine never backed up my Utilties like Disk Utility, even Terminal is missing.

I have got a bootable USB with the Mavericks installation app on it, but now if I run that is it going to wipe out everything that Time Machine did restore (my Adobe CC apps and plugins, for instance)? I would upgrade to El Capitan but I am using an old Wacom that doesn't have drivers for the latest OS X, so I am stuck for now (don't feel like buying a new Wacom just yet).

Any ideas on how I can get those utilities back without going through the re-install or upgrade process? I have looked at the old TM backups and they aren't there either. 😟