Jim,
I have AMD doors for my roadrunner. One thing I did notice is that the curvature of the door on top up front does not completely match the opposite curvature of the fender.
Also, up to in the back of the door needed some shaping/tweeking.
As far as panel alignment. When I initially installed the doors, I did so to the cars old quarters. Then I removed the old quarters and installed the new one's aligning them to the AMD doors. So, from that stand point, I can say they lined up to the old real well