Just boot from your win98 cd and let it install over the top. You will have to make your cdrom the first boot device in the bios.
You also will have to reload hardware drivers that arent included on the windows disk, so make sure you know your hardware before the install.
Its possible that this "dirty install" may not solve your problem. If your datas valuable, maybe bring it to a pro and try get the data moved or saved to a differant drive thru dos or some other method before ya make a move.