I wouldn't clone it. Just do a fresh reinstall (format) of Windows after backing everything up to an external, or a usb drive, or whatever.
You'll need to press *the* key (it varies) on bootup (delete, or one of the F#s, like F8 or F10 to get into the bios setup) - this is basically just the Motherboard's "settings"
Once you're at the bios setup, you'll want to change boot order so that it boots from CD first.
Once you've done that just restart your PC with the Windows install disk in, press "a key" when it says to press a key to boot from CD, and follow the directions
BAM you got yourself a fresh, clean, adware and virus free installation of Windows.
I like to format every few months anyway... keeps my box running light, and free of the crap that you pick up, even with careful use and an antivirus program.
