Actually, forget filesystem. It will just be more complicated than it needs to be, doing what I was thinking. Let's do a repair install. Boot from your Windows CD.
You will be prompted to "press F6 to install any third party SCSI or RAID drivers". Most users will not have to press F6, but if you are running RAID, SCSI or unsupported ATA controllers, then you need your controller drivers on a floppy disk. (This is important, in your case!)
Once completed, you will be confronted with "Windows Setup". You will be asked to setup up Windows, or repair Windows with the recovery console. Choose the FIRST option, NOT recovery console.
Choose F8 to continue.
Next, Windows Setup will find existing Windows XP/2000 installations. You will be asked to repair an existing XP installation or install a fresh copy of Windows XP/2000.
If no installations are found, then you will not be given the option to repair. This may happen if the data or partition on your drive is too corrupted.
That should be it. Windows XP/2000 will appear to be installing itself for the first time, but it will retain all of your data and settings. Just follow the prompts, have your CD-KEY handy and hope for the best!
Thanks to
AMDAthlon64X2, from whom I "borrowed" this simplified tutorial.