Found the answer.
Those plugs certainly indeed came in from behind...and were meant to come that way. Just like the one original plug I found still installed from behind. My 2nd plug was missing.
Here's where the confusion come in. The 1966 Ford factory assembly manual shows the plugs coming in from the front on other models (Hardtop and Fastback) if the Rear Seat belts were deleted. I then found a specific diagram (for Model 76 (Convertible Only) that shows the plugs being installed from behind, right on the bottom of the next page (Page 20). According to the Original Assembly diagrams, The plugs definately come in from the rear (Behind) ONLY on the convertible. The bottom view of Page 20 clearly shows this. Page 19 shows just the opposite for the Hardtop and Fastback. Why they did this just for the convertible is another bizarre Ford history question , but now there is documentation to prove it. The one original remaining plug that I had left in my car was clearly the original plug...as my Driver's side was missing. There was original paint (The original plug was painted over body color at the factory, and alot of original undercoating from the backside. Another mystery solved, Well sort of, We still have no reason why Ford did this just on the convertble, but that is the way that it was done in production.