Hi David
The holes on the picture in top are in my opinion not Ford Factory made.
The holes on the 2nd & 3rd picture are for junction blocs / connectors for wiring.
In TM 10-1263 you can see this in the wiring diagram no 7 and no 3.
Nbr 8 is the resistance for you B.O. driving lamp nbr 6.(on yours bolted in the left air tunnel)
Nbr 3 on top (right side) connectors are not fastened with round head bolts like the others.
I see your dog can't wait to go for a swimm
Bob