Agree the holes mentioned in the first post are not original
Bossbill, 1242 has a punched hole in that location. There is a nylon tie strap in that location (same as shock tower harness straps). The strap holds both the choke cable and the alternator gauge harness close to the firewall prior to their entry through the firewall. This is how I found my car - can't say if it is factory, but sure looks like that was original intention.
Makes sense that although Ford wouldn't use a hand punch to make a hole, Shelby would.
Its not
Holes was a product of the build process at San Jose so is shared with K code Mustangs built there
The strap at least is a reproduction and not original to the car. Originally there was a metal half clamp that held the choke cable not the wire or loom. Location of the hole can vary depending on possibly worker or when the car was built at San Jose
Of course found a number of examples where the prior owners repurposed the hole and different retainers to hold the Shelby wires, transmission wire loom or a combination of items
Examples from early through #2650