When this happens to me I bite the bullet and reformat the hard drive. I save all my data files to a back up and then reinstall windows. It usually takes a whole weekend to reload all the software and all the hardware drivers, but it’s worth it.
Then what you should be doing is working from a master image. IOW an image of a full installation with Windows and all your apps. Whenever you feel you need to do one of these dump and rebuild cycles, you just reimage your working hard drive from the master. When you install a new program, either do it on both drives or just on the master and then reimage the working disk from the master.
That's always been the way I looked at it. Once you knowyour system has been compromised, you can never again know that it isn't otherwise compromised by a stealthier payload vectored in by the one you discovered without a full format.