Try booting to your win2000 CD and choosing the installation repair option (I don't exactly remember the keystrokes, its been too long since I've reformatted).
Also, if you get a virus, make sure you clean it up before installing anything new. Just updating some software (other than your anti-virus program) won't help fix it.
Some resources for cleaning viruses are www.symantec.com www.trendmicro.com
or just google for the symptoms/virus name.