I have a guy at work that is telling me that for each of the manufacturing plants there will be differences in the Mustangs. So is a 1966 San Jose car different from a Dearborn car of the same year? I can see maybe the east coast put on an undercoating but that's about it.
The assembly plant never applied undercoating that was something done by dealers. And that practice depended greatly on where the car was delivered. Example Dearborn car in Southern Calif would not typically get dealer undercoating (or even know where to get it done) where a NJ built car delivered to Mich would likely get (for some extra $$'s) a good coating of everything
Lots of little differences but then there are many just between different months at the same plant
Things like different hardware, direction of bolts, differences in finishes (likely due to different suppliers) undercarriage colors, finish of wheelwells, trunk mat patterns all come to mind