I just went through a similar nightmare, only it wasn't due to a virus.
It started when I updated my ATI video drivers. And then updated DirectX and Media Player through the Windows Update. Several things seemed to be adversely affected by the updates and I tried to back them out. The ATI Uninstall utility crashed halfway through and really screwed my system up.
Imediatley after the crash, my system would not come up at all. Just a black screen and a single beep every two seconds. So I rebooted from my Win2K install disk, and did a system repair. Now I could get back in, but the registry was hosed so bad, that I was getting error about missing .msi files for prgrams that I had installed many months ago. If I started Internet Explorer, I got more install warnings.

If I opened the Add/Remove programs panel, I got the icons, but know text. Scan for Updates at Windows Update would freeze. Support for drives larger than 137 Gig was gone. For a while I thought I was going to have to write off a whole 100 gig partition.
I too found that I had to wipe the C: drive and reinstall Win2K.
I was able to copy almost everything the C: drive onto the other 100gig partition before hand. I too also had most of my software and data on the other drives. C: was mostly for windows and a few things that had been installed before I got the 200gig drive.
In the end, the only thing I lost, besidea a lot of time, was all my saved emails. I had installed Thunderbird on the D: drive, but I did not realise that it stores all the emails and profile stuff under Documents and Settings\(user name)\Application Data\thunderbird\profile.
Anyone want to reccomend a 3D card that is not ATI? I've had too many driver update issues with them, and TV out is really not an issue for me.