What is known is the rear valence, officially called "Extension Assembly, Lower Back Panel" by Ford, has several variations in its attaching to car. All did use 11 screws. Either the 2nd or 3rd screw from each end was installed on 64-66 San Jose build cars prior to painting to hold the panel to the car. Those "two" screws were painted body color. After painting, the remaining 9 screws were installed (along with the stud plates to the rear quarter ends) and were not painted. Other plants, and other time periods, used different procedures. As 65-66 Shelby GT-350's were San Jose built, they would be the same as regular San Jose production.
The screws used also varied. The 64,65 Mustang Body Assembly Manuals specify 380650-S101, which is a 10-12X3/4 Round/Washer head, Phillips drive screw, tapping. The 66 Mustang Body manual specifies 380934-S36 which is a 10-12X3/4 Pan head, Phillips drive screw, drill tip. Another head type found is the wafer head, mostly used for the "two" end screws. Phosphate and oil finished screws do not appear to be used.
If all 11 screws were installed at Dearborn and/or Metuchen prior to the car being painted, they would be body color.
(Note: service replacement specifies 380934-S36 which is a 8-18X1/2pan drill tip screw. It's a bit small for existing holes on 64 and 65.)
Jim