Bill,
In this case I will state that Ford Car Parts (aka MPC), is a service replacement document and does not always reflect what was used on the assembly line. However, it's a Shelby, and from what I understand about the practices used at the Shelby facility, anything that worked was used.
THEY WERE NOT BUILDING CONCOURSE GRADE CARS.
That bolt, 359662-S, was Ford's common replacement for all fender area bolts and a host of other 5/16/18 bolts. In this case, I would be more inclined to use the 67 Mustang Body Assembly Manual. That statement is based on a simple after the fact assembly line principle - what "they" took off, "they" put back on.
Jim