I thought some Shelby Mustangs had their VIN stamped into the motor after 'rebuild' at the Shelby facility. And FWIW, when I had my C4 out of the '68 Mustang early this summer it had the VIN number stamped onto a cast flat spot on the passenger side of the case, right above the vacuum modulator.
But generally, so long as the casting number is older then the car (and very rarely younger) and the cast in build date is within 3-6 months most people consider that 'matching numbers' for a Ford.
-ron