OK thanks for the clarification, I was kinda scratchin' my head on that!
Yes, FRST rocks, is continually updates, and FREE!!!
Here's a link to a tutorial on the subject.
FRST Tutorial - How to use Farbar Recovery Scan Tool

I also routinely use SFCFix by Niemiro (Sysnative Forums), its similar to sfc /scannow with additional replacement functions, via, fix scripts, for registry entries, missing or corrupt cat, mum, and manifest files, etc. It takes permission from Trusted Installer, performs the operations you institute and restores permissions. If you've ever tried to do the permissions thing manually, it's a nightmare to do on a regular basis. No documentation to learn how to use it though. I've spent countless hours reading Sysnative Forum posts to gain understanding on how to use it's functions.

Nic