I got corrupted system files

I hope I got this posted in the right place and hope I got the right title. I started off with the SoftwareBundler:win32/WinOptimizer virus today and after getting that fixed/removed I found out I had some other issues going on so I found a site for trouble shooting windows and I tried to do a system file check through their instructions and found out I have some corrupted files. When I tried to fix the problem [following their instructions all I kept getting was access denied on all files and their instructions suggested I reset the permission by activating windows again.

Does that mean I have to reactavate the windows product key? if it does then I tried it and it will not let me do it.
Sorry I am not very much of a techie person. All I know is I am on windows 8.1...64bit

Rather than trying a 3rd party site I would run sfc as described in this tutorial:
http://www.eightforums.com/tutorials/3047-sfc-scannow-command-run-windows-8-a.html




Edit: I would do Option Two first. It is simpler than at boot and may tell you the system files are OK.