"Nice and flush with a good gap until the door is opened". If you check the shop manual, you will find that the door is to be adjusted to be flush to 1/16" outward of the cowl to prevent interference with the door seal upon opening of the door. They say to bend the hinge to correct this. I notched the holes in the part of the hinge that bolts to the cab to get my door to have a 1/16" outward position. I was scared to mess with bending the hinges. Have you rebuilt your hinges? If not, you should start there, as that will most likely change how things fit. And if you are lucky, maybe to your favor. Of all the things that I have done to my truck, I am most proud of how my doors fit and close properly. It is not an easy thing to accomplish!
