I did end up backing up and re-installing the system, so I've been tweaking everything all day today so far. Next step is definitely making some kind of image or boot disk to store externally in case this happens again. Thanks again to everyone for your ideas.
Are low level formats still advisable for newer disks? I recall reading that they are no longer necessary for newer hard drives. Last time I had to restore my hard drive from scratch I got the impression that a command like FDisk at least for a Windows system was obsolete. As stated already Acronis True Image or Norton Ghost is the way to go for backups and restores now. Might be useful to create a boot CD too.
I mentioned low level format earlier, I was just referring to the choice of "quick format" or "format and lose all files" that comes up when installing windows XP. I can format and lose all files and reinstall and have everything up and running in 3-4 hours. I keep a folder on the D drive with installation files. After that I tweak things as the need arises, it works out ok. I used Norton before, it keeps records of restore points but you can't tell what was done to cause the restore point to be set, you have to keep your own record, one more frigging thing to think about... if Acronis tells you what the setpoint was about or even had a space for a description I would use it. I don't recall that Norton had that at all... most people recommend Acronis on ET.
For future reference keep this page handy http://www.kaspersky.com/removaltools They provide FREE virus removal and they removed stuff from my computer that others couldn't.. They also have FREE virus scanning. And here is another excellent FREE virus removal with a more updated list than the Kaspersky one I linked to above http://www.avast.com/eng/avast-virus-cleaner.html
Not sure what you're meaning to say, but "quick format" and "format and lose all files" ... both result in erasing the hard drive... well almost. But low level format is different from either. Low level format would be used when you had a virus corruption... seems it would be a good idea also when changing operating system.