Work forward from the rear quarter panel. Even if that has been replaced it's hard to put it in the wrong place.
Use the front edge of the quarter to align the rear edge of the door , you want a parallel gap with the swages in line. This is what the shims are for , a shim under the lower hinge will raise the rear of the door and close the gap at the bottom , removing a shim from the top will raise the rear of the door and and open the gap at the top.
When the gap is parallel raise or lower the door to get the height right , you want a good gap on the sill.
It's a bit of a juggling act but can be done.
Once you know the door is in the right position it will help you to to determine if the A panel is wrong.