Funny, the craze over VIN matching drivetrain seems to have infected every corner of the hobby. I see where it is vital for Corvettes and Chevy's where there is no indication in the main VIN what motor came with the car. In NCRS juding, you cannot Top Flight without the VIN present (that is the reason many today are restamped). The "K" in the VIN means that this is an original hipo 289 without question.
As we all know, VIN stamping did not become standard on all FORD engines until the 1968 calendar year by government mandate. Ford chose to hand stamp the VIN early performance motors to reduce theft. Most of them did get the stamp, some did not. It is date code correct with NO vin stamp (rather than the wrong vin stamped). This being a very early car, it is reasonable to conclude that this car's engine was not stamped into the motor and that this it is original to the car. I doubt it would even cost a juding point. True, the car could be more valuable to some with the VIN present, but that does not make the car any less genuine.