With Windows 98 you may actually need the Windows 98 Startup Disk, it's just a floppy bootdisk with needed files and CD-ROM drivers. It can be freely downloaded at: http://www.bootdisk.com/bootdisk.htm
To reinstall Windows 98 when using the Windows 98 Startup Disk: 1. Insert the Windows 98 Startup Disk, then turn the computer on.
2. When a menu appears tell it to load with the options to start with CD-ROM support. 3. Then once the command prompt appears type in your CD-ROM drive letter and then setup.exe. Example: E:\setup.exe
Replace E: with your actual CD-ROM drive letter, and do note in MS-DOS mode drive letters can be bumped around and change.
Edit: Before attempting to reinstall Windows you may want to try starting the system using the Startup Disk! That way you could backup any needed files first, etc.