|"I am booting from the HD, then using the CD to re-install"|
That's your problem. You need to boot directly from the CD. Here's the WinXP repair instructions, Win2K is done the same way:
Hopefully you have the product key because you're going to need it. And hopefully you realize that the repair will wipe out ALL Windows updates that have been installed over the years.
I don't know why you've refused to state which OS you plan to upgrade to, but by doing what you're doing, you're just making a whole lot more work for yourself.