OK, have you done in-place upgrades/resinstalls only? or have you uninstalled+new install. If this keeps going retro on you, you might want to wipe. Are you going to do a fresh reinstall of everything? Sounds like lots of work. There are config backups in Win98, but I don’t recall path off top of my head (I’m sure another reply will). I’d backup any important stuff, drivers, apps to a thumb drive or burn a CD to make reinstall less horrible.
On a bad note, I’ve seen spyware that will auto-undelete, poly-morphic, stealth, dynamic file rename/relocate (but probably not to restore Win98 %-O ). Be sure system is real clean, not just AV, but anti-adware/spyware also.