After cleaning up and deburring the hinge, I carefully installed the new brass bushings (remember there are two per hinge). | 
And now the new hinge pins can go in. I applied a small amount of grease to them before driving them home. | 
To avoid tweaking the hinge, I firmly held a big hammer on the other side of it to equalize the blows. |
Now the new door check spring can go on the top hinge. Lubricating the pivots will help eliminate squeaks. | 
For good measure, I chased the threads of each door hinge bolt before putting the doors back on. | 
Look how much of a difference the new hinges made! (They brought the whole door up about 1/4-inch in the rear, but don't install the strikers yet). Now we need to adjust the door on the hinges to bring it back down since the gap around the door is uneven and it hits the cab. |
Front, back, up, and down adjustment will be done where the hinges bolt to the doors. By loosening the three bolts on the bottom hinge, the door will come down and slightly forward at the bottom. A floor jack with a piece of wood on it will come in handy to help support the door during adjustments. | 
Looking from the side, that little adjustment at the lower hinge got things real close, but the door needs to be aligned on another axis as well. The top of the door is too far away from the body so much that it's almost even with the rain gutter; notice the uneven gap on the A-pillar too. | 
We adjust this at the hinge and door jamb. By loosening the bottom hinge bolts and jacking up the door a small amount, it will pull the bottom of the door out, and as a result, push the top of it in. If the whole door needed to come in, both hinges would be loosened and the hinges moved closer toward the inside of the cab, one at a time. |