After running sfc/scannow, everything will bounce back to windows default , and all the patches will be reverted . So now run universal theme patcher as admin (right click > run as admin) and apply the three patches , and restart the machine . When it starts , put the theme (the folder containing en us etc and the .theme file only) in the resources > theme folder as per the Theme - How to Apply Custom Themes
tutorial , and then apply the theme .
There is an alternative method to do the same , that is Enabling Custom Themes - Windows 7
If you want to replace the system files with the custom ones , I'd suggest you to have a Backup Complete Computer - Create an Image Backup
at first (that's must ! If you get in any trouble in the process, it is the easiest way to get rid of it ) and use System File Replacer
for replacing the files like explorerframe.dll.
If there is any further problem, post back . Applying theme is not such a tough job .