Chuck,
let me first say that I really have enjoyed your website. I will be putting all the panels in mine eventually and your photos are really inspiring.
I have been noticing the door out at bottom/back on a number of show trucks myself. In these cases, the door meets the cowl correctly at the front but sticks out at the back. I think the contour of the door is the same both at front and back and to me this means that the angle of the front cowl/doorpost is wrong. I made up a little cardboard form to study the contour to make sure it is the same. I think this happens in a lot of re-build cases because the angle of the front doorpost changes as the cab weakens and bends. then if new panels are added in at the same angle, the problem remains. I have seen one truck that someone attempted to reshape the door frame around the window to compensate and it didn't look good.
I look forward to see your final pictures when it hits the street.