The vfat message means the system has lost track of its file structure. Presumably the anti-virus programme has taken out files that, although infected, had a big part in running the system. Forget about getting it to boot for the moment. As you have important data to be rescued, slave the hard drive up to another PC which is fully updated with anti-virus software. You can then rescue any data you want. After that, if the PC is worth keeping at its current specification, you can fdisk the drive, format it, and then re-set it with Win98.
If you need help with any of the above, just ask.