Did you try booting into Windows 98 Command Prompt Safe Mode?
Boot into the command prompt safe mode, and run scanreg.exe or rename the system.da0 as system.dat (this should restore to a local backup) make sure that you do this:
cd c:\\windows\\
attrib -s -r -h system.dat
copy system.dat system.bad
copy system.da0 system.dat
attrib +s +r +h system.dat
But run scanreg.exe first to see if it can fix the registry.
This should back up to the previous registry, your current one will be renamed as system.bad if you want to inspect it later. You can always copy it back later.
Also sometimes if "shift" is held down while booting, it bypasses the default settings.