Tony, what ORAC is saying should work; you'll have to get rid of any autoexec.bat and config.sys files from the old setup. There is a neat DOS program that Dell gave me called deltree.exe for the express purpose of getting rid of a corrupt Windows setup. It deletes a Directory (eg Windows) and its tree of sub-directories. (Hence the name deltree). It allows a clean install of Windows without formatting the HD.
But don't imagine that everything is going to be as it was before when you've rebuilt Windows 98. None of the currently installed programs will work because you will have an absolutely clean Registry. You are going to have to re-install all your Applications.
Your data should remain intact, however.