Well guys, I finally nailed the problem on the head today (mind you, I could have last week if I wasn't so lazy):
CCleaner (and any other registry cleaners) that scans for invalid shortcuts or application path references will delete three keys required by Windows 8 to display the metro CP, Windows Store and metro Remote Desktop. These keys are as follows:
Please note that in CCleaner, the problem arises when the user scans for invalid Start Menu/Desktop shortcuts from within the cleaning dialog, not the registry scanner.
C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Windows Store.lnk\C:\Users\Mitch\Desktop\notused
C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Immersive Control Panel.lnk\C:\Users\Mitch\Desktop\notused
C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Accessories\Immersive RemoteDesktop.lnk\C:\Users\Mitch\Desktop\notused
So when using ANY registry cleaning software, be sure to look through the scan prior to removing keys and UNSELECT these three "invalid" shortcuts. Although, I still don't understand why this made the apps completely inaccessible (via some external links in the normal CP, etc) and quite frankly, I don't care.
Thanks for your help guys, and I hope this solves the problem for others as well