I have a pretty good way of aligning doors that have a quarter mile of adjustment on them. I got the idea from Dodge vehicles. From the factory, the doors have one threaded stud on each upper and lower hinge. The other is a threaded hole. The factory glues washers onto the hinge opening that accepts the stud. The washer has the same inner diameter as the studs outer diameter, so all you have to do when hanging the door is slide the studs through the washers and tighten the nut down. Then thread the two bolts into the other holes and you're done.
Now, not all doors are equipped with studs as most doors use only bolts through the hinges. What I do is take a washer, grind the back side to rough it up, and apply a small bead of epoxy to the backside of the washer. Once I have the door fitting exactly how I want it, I remove one bolt from each hinge, slide the washer onto it, and run it back in nice and tight. When the epoxy is cured and the door is ready to come back off for paint work, I pull the bolts out and remove the door leaving behind the glued on washers. This helps tremendously when reinstalling the door and it always lines up just the way I want it to.
Now, you may not want the washers on there permanently, so all you have to do is when all the bolts are nice and tight, only remove the two that the washers are on, and simply tap them off with a hammer and punch/chisel. Then run the bolts back in and snug them up. Its a great way line up hinges to doors/cowls/pillars without having to scribe, or punch into the metal, or drill extra alignment holes. Just be sure to use a strong enough epoxy that won't break loose while hanging the door!
Good, Fast, Cheap, but you can only pick two!