What should I do?

I'll try and keep this brief. I've had Windows 7 x64 Pro for about a month. It worked great.

Until I used a program called final uninstaller. I removed some vital system files. Don't know which but Itunes didn't work. So I did a "upgrade" of windows 7 x64 Pro with a copy I made of my windows 7 x64 (It's legit).

This fixed the itunes problem and seemed to get things working at first. All my firewall preferences where erased.

But, for the last few days my system has been freezing when exiting games, and multi tasking. Some websites will not open at all. This has never happened to me before. I have run nod 32, malwarebytes etc and didn't find any problems.

My question is should I just do a clean install?

Or

Should I try to do reinstall a backup I did before using that final uninstaller program was used and I did the "upgrade". (This backup was done with windows 7) Thanks for reading.