You don't run FAT on Windows anymore, it's some other file system I believe (you can, but its slower). *EDIT* You run NTFS on Windows 2000 and newer.
Anyway, the easiest way is to run the Windows disk and it will prompt you for a format and reinstall. Just poke the buttons and sit back an enjoy. It's so simple, even a caveman could do it.
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'13 Mustang 3.7V6 - MT82
'00 GP SE (L67 Swap, XP, Headers, 3.25")
'98 GTP, '01 Bonne