you might just have to format the machine, make sure to get backups of all your data that you want to keep, make sure you have all the drivers and such. start up with a boot disk and type
format C:
say yes, let it format, when it asks for a volume lable just press enter for none, then type
D:
to change the directory to drive D: (most likely the default cd drive when booted from disk)
and type
setup
and it should take you through the setup. If setup doesnt work, type dir to see a listing of all the files on the cd and look for one named setup/install or a folder called 98se and type cd 98se and look for a setup/install in there (i know on my 98se disk i have to navigate for the setup)