I assume you are able to boot from floppy in order to get to the stage where you run scandisk. Instead, type
I suggest that you then run scandisk agian from the DOS prompt to make sure that this has repaired the FAT problem. If not, you will need to run FDISK to delete all partitions and then create them afresh - you will then be prompted to re-format c:\. Test the FAT again with Scandisk, to make sure you don't have a hardware prblem.
Assuming that you have installed your CD driver from the floppy, you should now be able to re-install windows without further ado.