Windows 98 Second Edition has the DOS setup disabled by default, so you can not do a clean install from a newly formatted hard drive. To get around this, follow these steps:
1. Start your computer using a Windows 98 boot disk with CD-Rom support 2. At the command prompt, type 'A:\Fdisk' to create a new hard drive partition 3. Copy the Windows 98SE install files from the CD-Rom to the new partition 4. Install Windows 98 original build from the CD-Rom 5. Run the Windows 98SE setup and create a boot disk when prompted 6. Reboot to DOS using the Windows 98SE boot disk 7. At the command prompt type 'A:\Format /S' to reformat the "C:" partition and then copy the system files to the "C:" directory 8. Remove the boot disk and boot back to DOS 9. Run the DOS based Setup from the "D:" partition