The registry and file permissions repairs are ran and put back to the defaults, and the windows defender registry key was put back to its default, I took a screen shot of mine to show what the default is
My permissions tool use to give you full control which fixed a lot of things, but in Windows 8, when you do that will completely break the app store. Windows 8 is the easiest OS to break. So the only way I could properly fix Windows 8 with permissions was by restoring the default permissions.
But, I have ran the repair tool on a ton of Windows 8 machines and never got the errors you did, so I am curious what the difference is.
How is everything running right now?
Shane