You can run this though maintenance should have cleared whatever it could from the drive
Double click my computer then right click C Hard drive, click properties, click disc clean up then post the used and free space figures
This will rebuild rather than restore the registry and also replace missing or corrupt system files
Boot the PC and keep tapping F8 right after the beep until you get options, select command prompt only, type scanreg.exe /fix then press enter, it will run through a few screens then say registry repaired. Press enter then press ctrl + alt + delete keys together to reboot.
When Windows has loaded, click start, all programmes, accessories, system tools, system information, tools then run system file checker and replace any files it asks for from the 98SE CD then reboot.
When it has loaded to the desktop, click start, programmes accessories, system tools to run disc clean up, then run disc defragmenter from system tools