Just to continue the discussion .... really
".....there isn't one judge that knows everything there is to know about your specific car,"
More the reason to get involved and educated others about the changes that came during production.
"mostly due to the fact that Ford was SO inconsistent."
Would suggest after 30+ years of owning these cars Ford was more consistent than not. It’s interesting to see owners who "know" there car came that way. Why?

"Because I know so and that's the way it was when I bought it/the first owner bought it ......
"So if your car's widget is green and the judge "knows" that it is supposed to be blue, you have to prove that yours was originally green. You might know that it was green but you can't prove it."
Back to the "the owner know it" If there is nothing to prove it how does the owner know that's the way it was? If you know something is going to be an issue do some homework and bring it to the show to educate and share with other owners (their looking at your car) and the judges. It’s not very likely that yours is the only car built that way. Instead we tend to see mini-trends. A worker who choose to do something different, do to their height, size, ability or laziness. But in general they tell us that they tended to pick something and stick with it...... unless they were screwing with the inspector or another worker
"So points are deducted (usually leading to extreme agitation on the part of the owner)."
I would offer that in almost every case were a point was deducted for something that should not have been deducted for there is another item that the judges did not catch. I always figure it works out as an even trade. In fact we miss much more than we catch generally. But some owners only want to complain about the thing the judge did wrong
".....So IMO I have two choices (1) show the car and deal with the inconsistencies of the judging,"
Or you might want to phrase it as the inconsistencies of the cars and owners
Judges not perfect.... you bet. Have people at every show that are more than willing to tell us so. We do the best we can with the understanding we currently have. Good judges never stop learning but most have seen enough cars and details not to except that rules and judging should change just because one owner or car is restored differently from the current understanding. I don't suggest that we ignore this "new" detail but if we changed the rules every time we get told "my car came that way" car show participants would have a real bone to pick with us.
Not wanting to sound defensive argumentative - we've lost many good judges through the years . Loosing each has set the hobby and the understanding allot IMHO
After 35 years of judging I'm always happy for an opportunity to discuss the in's and out's of the process - Thanks Bob for the site