I am not trying to fan the flames here or saying you are wrong, however when I first hung my fenders, the drivers side (door skin and fender) did exactly what you are saying; the bottom lined up and I could get the top line aligned but the center style line did not line up at all. At first, I was thinking exactly what you are saying, however after some research and talking to guys who have done a lot of Ebodies, I went back to adjusting and shimming and interestingly enough it came together and lined up. a large part of this is sequence and understanding that a few things; these cars were far from perfect when new; they are put together like a model car and done so by humans, thus not perfect; no repop is going to fit every car exactly the same and lastly, there are many components/adjustments that have a variety of results. In my case, the bottom of the fenders did not fit the pinch weld correctly; most of this was due to past damage and efforts to repair the damage. That said and in reference to that center line; I found that shimming the front bolt of the lower/rear part of the fender (the part with 2 studs that hold it in place) along with tightening the top of fender (using the inside stud) made the fender bow out next to the door and line up.
If I think of it, I will take a measurement and let you know. Having said that, I seriously doubt AMD is going to change a stamp/mold, very expansive endeavor.
