I see no reason why you could not still use a fastback body kit since everyhting from the kit would be the same with the exception of the side scoops and deck lid.
Look at the 68 Shelby GT-500KR convertible. It was absolutely beautiful.
There are a lot of places selling the body kits out there and easy to find. Try your typical mustang parts house like "Mustangs Unlimited", "Laurel Mountain Mustang", and "Mustangs Plus"
'66 Ragtop, vibrant red, 289-4V, 4-speed toploader
'68 Fastback, space blue metalic, 351C-4-V, 4-speed toploader
'69 Mach I, (Pending Resto Project)
'66 Fastback (because I wanted one)