It seems to me that what you did was an upgrade. This does not change installed programs or user data. In order to do a completely clean install of Win 98, you need to format the C: drive first, then install as new. If you have problems booting from the CD you'll need a Win 98 startup disk. You can make that by inserting a floppy into the A: drive and then go to Control Panel -> Add/Remove Programs and click on the Startup Disk tab. Once you've got your startup disk made, give it a try by restarting and leaving the disk in the drive. When it begins to start, tell it to start the computer with CD-Rom support.
If that works, then type format C: from the DOS prompt and it will take a little while to format. Make sure you've got your install key. Then you can re-install Windows by putting the Windows disk in the CD-Rom and typing in E: setup. If you are using an upgrade disk, it will require that you have an earlier disk to insert during the process, such as Windows 95 or Windows 98 first edition. If you don't have an earlier disk the install will not continue.
Edited by Herk, 27 April 2005 - 04:41 PM.