Sounds like you know more about this issue than I do. The question is, can you use win xp on your system at all?
If not, the easier solution may be to install your drive into your roommates system (as a secondary drive in the system) and backup important files to DVD. Of course, you will need to have access to a DVD in your system to restore the data back into XP after you re-install it. As long as you are sure that the drive itself is OK and not failing.
If you have access to XP, you should be able to mark your directories as share directories, then use your roommate's system to fetch the files that you need to DVD from Network Neighborhood from the Windows 2000 box.
Alternately, download the files that you need to a directory on the 2000 system and burn the DVD backup.
Do you have access to a DVD on your system?
The other option, would be to do a repair installation on your system. But, I can undertand your need to back up the files first.
Just how to do this in Knoppix, I don't know, but I am willing to look at it and see what I can find.
Perhaps, others have better ideas.
Take a look at the following links that may help, as well;
http://hex.zapto.org/pages/2004/jan/knoppix_recovery.phphttp://www.shockfamily.net/cedric/knoppix/