A number of years ago, Norton offered an option for making a mini-Windows CD. That is, a CD that booted into a Windows environment and had all the users settings and important drivers, so the CD would run the computer as a Windows OS.
It seems that now, more than ever, we need something like that, to combat the malware being created.
From such a malware free environment, we can scan the fixed drive for known malware. The software can do the kind of clean-up that would be impossible when it is fighting off an aggressive rootkit or its droppings.
Perhaps, we can create bootable portable drives that contain the same Windows environment. I don't know where the 0-sector comes in when one is booting from a DVD or a portable harddrive, but it would seem that if the BIOS says to boot from the DVD or external harddrive first, then it should be a clean boot. And, in the case of the DVD, it would not be subject to modification.
I remember hearing that there were copyright issues. Maybe it's time to engage MS in litigation -- if they will not properly protect our computers, then at least they should give us the means to protect it ourselves.