[rpmerf]

Wanted to post a follow up in the event someone finds this thread in the future. I managed to get the doors aligned. I did end up using 1/4" worth of shims (fender washers) on each side between the top washer and the body.

Process I used:

Remove striker.
Loosen up the 6 bolts on the pillar.
Jack up the door near the hinges to get the door up as high as it will go. Rock it back and forth a bit to make sure it is all the way up.
Tighten one bolt on the bottom. Remove jack. Pull the back of the door down to move the top hinge back.
Tighten one bolt on the top. Loosen the tight bolt on the bottom. Pull the door up to pull the bottom mount back.
Tighten up one bottom bolt.
Close the door. Look at gaps and body lines.
Repeat the last 3 steps making tiny adjustments until it looks right.
Install the striker. Adjust up / down to get it to close without moving the door or hitting the latch on the door. Adjust in/out to get it flush with the cab.

I decided I needed to shim the front cab mounts because the the door was aligned with the body lines, but it was close / hitting in the bottom back and at the top of the wing window. With the shim, the gap is better. Maybe not prefect, but it is not hitting anywhere.

Overall, I think the doors close better than they ever have. They have been really hard to close since I installed new door seals ~5 years ago. The doors were a bit far forward, so I moved them back. This makes closing on the door seal easier.