I always leave the hinge screws loose enough that you can close the door and gently move the door to its proper place, then slowly open the door to tighten the screws. Once the door is done then go to the latch . Same deal , but you can usually see where the wedge will go equally thru the two guides. Also make sure you have the proper shim under the B post latch or you will cave in the aluminum. I always use the original alum as a guide to see if the holes were rounded out more for placement of the latch ( hand built you know)
Also if you are using new striker plates, they are different from the originals and require more work. USE ORIGINAL shaped screws as the new ones have been known to be oversized in the head and can bind on the latch when closing , go slow with closing the door. Always use a little masking tape to protect surfaces when in doubt. Closing the door if done right should not have to be closed hard, check the door seals first, oversize padded door panels also give headaches, see why restoring a car can be so much fun ???? !!