I purchased both doors new for a 68 coupe. Trouble is the drivers door does not line up with the rear quarter. Is there a "secret" method to geting these to line up.  

I replaced doors on my 70Mach1 and I found the easiest way to line up the doors was to loosen the attaching bolts, the fender bolt @ the door jam and the door latch bolts and then just start trying to tweak everything into place. Otherwise, the door may match the quarters but not the fender, etc.