Do you have the door weather strip installed on the door? This makes adjustments difficult, especially in your case since you are installing a "new"-to-the-truck hinge.
When adjusting a door to the door opening, it is best to do it without the striker installed. It gets in the way.
Are your door belt lines lining up with those on the cab, front and back? You can solve bad gaps by moving the door up or down because the doors are slightly wedge-shaped (narrower at top than at the bottom).
You can get away with a tight gap at the front edge of the door by adjusting it so that the leading edge of the door is 1/16" proud of the trailing edge of the cowl (Factory spec is "flush to 1/6 inch out from the cowl). This will give you a bigger gap at the rear to solve your contact there. You can accomplish this by either bending the hinges at a specific place (don't ask me where, I don't know), or by grinding slots on the bolt holes of the hinge half which bolts to the pillar.
Ain't doors a gas?!
Carl