Hey stephenn,
Windows 98SE ??? That is a dinosaur of operating system

.....well, when you see your computer going through scan disk one every start up it should tell you something......something is wrong ? helpfully you don't have any bad sector on the drive, if so, it would mean the data on those sector will not be recover-able.
I could suggest to re-install the operating system on the top of the one you have but if your hard drive is dying , it would make the matter worst.
My suggestion is to transfer the data to a safe location first then worry about the hard ware. if you can plug your hard drive to another computer and transfer the data and burn them to a DVD of CD.....then you may want to invest a bit on money and get yourself a new computer [they run around $600 ~$700.
Cheers