Door alignment issues
Up & down is controlled by hinge to body bolts; in-out controlled by hinge to door bolts.
This is exactly what I was going to post. That's right on the money.
When adjusting I put all the bolts in but just work with two at a time (mostly when the situation allows).
For example: if you are doing "In/Out", all 4 bolts on the door are in but only the top and bottom bolts are tight enough to keep the door from moving.
Loosen the bottom bolt (on the door), rotate the bottom of the door in/out until it lines up with the rocker, then tighten it.
Now, loosen the top. Rotate the top of the door in/out until it lines up with the quarter.
This process may need to be repeated. Use this "Walking" method until things line up.
I like to remove the striker when adjusting a door, hood, or trunk lid. Others may not.