I can only suggest that you try installing Windows over itself. To do this you will need to enter the BIOS. Typically when you restart it will say "Press DEL to enter setup" - which key(s) you need to press depend on your motherboard - some examples click here
Once there, navigate the screens until you find boot order and change it to CDROM as first device. Exit the BIOS, saving your selections.
Place your Windows 98 disk in the drive and reboot. Follow the on-screen instructions.