The assembly manual calls for part# 357903 as the screw to attach the kick panels. This part # is a 1/2 in screw. All the screws that are in my 65 are 3/4 in. They look like part # 375876 which are the 4 screws to hold down the front carpet. Did Ford change their screw requirement or would the assembly line use what they had handy?
Part of the confusion is the incomplete hardware part numbers. That might give part of your answer. The kick panel uses 357903-S8, a zinc plated screw 1/2 inch long. Other uses for the same screw with a chrome (-S13) finish were also used (on Fastbacks and for the rear interior quarter panel on Hardtops) and a phosphate and oil (-S2) finish used on convertibles and on all hood seal ends. The other screw, 375876-S2, is only used with a phosphate and oil finish to mainly hold down the carpet. There is one major difference between the two (besides length), 357903-Sx has a head diameter of 3/8 inch, while 375876-Sx has a head diameter of 1/2 inch. A more realistic possible "replacement" screw is 350075-S8 which has the same head diameter as 357903-S8 but is 3/4 inch long. Seven were used to hold the glove box to the dash on 64 and 65 Mustangs. In 1966, the glove box used the same screw but with a phosphate and oil (-S2) finish.
Jim