The good thing is that if you use the door hinges to align the rear of the door to match up to the quarter panel (probably loosen the bottom up slightly and carefully adjust), then you can adjust the bottom of the fender slightly to match the front of the door without messing with the hood gap (since it will likely cause the fender/door alignment to change).
Also, if by adjusting the 'tilt' of the door causes the door to stick out or pull inward (at the door/quarter panel junction), you can adjust the striker inward/outward slightly to compensate.
It'll take a lot of trial-and-error to get it right. Don't take too big of swings at it and you should be fine, but you most likely won't get it perfect the first try.
Before you start, make some alignment marks with a dry-erase marker or grease pencil on the hinges and their mounting surface so you can put it back to where it is now if you can't get it right (then remove the markings once you're done).
I'm no expert at this, but that's what worked for me.