Doors are a pain, that is for sure.

Some very good hints so far. I can add:

1.) Get the hinge line as close to the upper skin as possible. The first photo is of the cutout for some Tam offset hinges (my favorite).

2.) Have the most clearance between the hingeline and the door opening, especially if the skin material is thick.

3.) Bevel the inner edge of the door (the one near the hinge), especially important if the skin is thick.

4.) Line up the hinges with a wire and if possible leave the wire in as the hinge and you have a removable door (a must if you ask me)

5.) Outer doors can use a little skin mount hinge made of brass tubing and music wire.