You have just encountered the biggest problem with AMK hardware, the head markings. Those shorter bolts are functionally correct and probably exact as a service replacement but are not the same a factory originals. The head markings that you are concerned with are grade 5.1 which, for the most part, was not used on 1966 and earlier Mustangs. I think grade 5.1 hardware started to be used in 1967 and on. I am looking at an un-opened AMK hardware kit, F-304, for cast iron water pumps and I see what you're concerned with. For reference, grade 5 was used and the head markings would have a dash at 12, 4 and 8 on the North American round dial (I think down under would be 6, 10 and 2 -
.)
I'm still eating breakfast so give me a while to check head marking on my Oct 65 San Jose "K" Fastback.
Jim