Yeah ecniv, that's what I said. sometimes the quickest solution is to start over.
Dave, you can boot from that CD it will ask you to "press any key to boot from CD..." and then you just hit the space bar there. Let it go through it's little routine and it will ask you what you want to do, choose install. Then it will ask you what partition to install on.
At that point choose c: drive if that's where you want it, or wherever the 98se is installed. Then press "D" for delete. This will effectively blow away all of your data, so make sure you copy what you can.
It will prompt you to click "L" if you are sure you want to delete the partition, then you will get the opportunity to format the partition. Like ecniv said, choose NTFS, quick format.
Good luck and let us know how it went.