In short, No.
The registry is not compatible from 2000 to 98, so you essentially have your near-normal clean install of the OS. No software or prior setting will survive.
The issue of the file system being compatible may be an issue as well. If it's NTFS, then Windows 98 will not install. Partitition Magic can convert NTFS to FAT32, but the loss of programs and settings is certain.
Bob
I have the Win98SE OEM disk and the Win98 Upgrade disk.

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic