You probably have the Windows 98 CD which installs aided with a floppy disk... so, you can make a bootable copy of the Windows 98 CD, using PowerISO (or InfraISO, MagicISO, or Freeware Windows Bootable Image Creator)... to copy the Windows 98 CD and make a bootable ISO image that you can burn onto a bootable Windows 98SE CD. PowerISO can burn the ISO or do it with a CD/ISO burner. I find IMGBurn easy and failproof.
http://www.poweriso.com/
http://www.poweriso.com/tutorials/make-bootable-image.htm
http://www.imgburn.com/
http://www.imgburn.com/index.php?act=download&
Instructions to make Windows 98 non Bootable CD into a Bootable CD copy:
In PowerISO > New > Data CD > Next Add > Browse for the Windows 98SE CD contents > Select all files and folders in the CD > and click Add...
Next from the Action menu > Boot > Add Boot Information > Here you will need a bootable CD to get the bootable information files from with ISOBuster
http://www.smart-projects.net/isobuster.php , or download the boot information file from this link
http://sourceforge.net/projects/bootinfoscript/?source=typ_redirect So, after Add Boot Information, browse to the boot information file, select and click Add... your image will become bootable and Next click Save and Next click Burn or burn the saved Windows 98SE bootable image with IMGBurn or he burner of your choice.
Note: PowerISO can be used to make images of up to 300MB.. if your Windows 98 CD is larger it will not be helpfull... in that case use IMGBurn or Windows Bootable Image Creator to make the image and burn it with IMGBurner.
Windows Bootable Image Creator
http://www.freewarefiles.com/Windows-Bootable-Image-Creator_program_75008.html