When you ask which one is the rarest, you might want to establish what criterion should be factored into the equation. I think everyone would agree that pre-production prototypes and test mules should not be included.
Whether it be a Ford Mustang or any other marque, it is generally accepted that the minimum criterion for gauging a car's rarity should include the:
>> year, make, model, body style and original engine.
To narrow it down further, some might also want to factor in transmission. Others will often factor in paint color, trim and/or other options.
Using the minimum defined above, the rarest Mustang of them all would be VIN 7R03Q133290. Decoded and verified by Kevin Marti, that translates to a:
1967 Ford Mustang Convertible with a 428 cu.in. engine.
This was a standard assembly-line built Mustang at Ford's San Jose plant.
All other big block Mustang convertibles were the S-code 390 cu.in. This is the only one to receive the dual-quad topped 428 cu.in. "Interceptor" engine.
It was ordered by and delivered to Shelby American where became Carroll Shelby's "personal driver." It was the only Mustang convertible ever ordered by and upgraded by Shelby American (the four '66 GT small block Mustangs were a creation of a California Ford-Shelby dealer).
web source:
1967 Shelby GT 500 Convertible - The World's Rarest Car