2 things:
Why are you still running Win 98?!?!?!?
Second, dude you better get IE working or you won't be able to do windows updates. Ummmm....do they still put out updates for Win 98??
Take your Windows 98 CD and re-install it over top of your copy on the HDD you have now. It will will fix any corrupted files and replace any missing ones leaving all your programes in tact.
For you Win XP bunch do a sfc/scannow from the "run" command to fix corrupted system files