I do this for a living on freshly built cars
where the hinge plate adjacent to the door sets the general door height and body flush point on the door, at that point. as for the rest of the door. (not for the faint hearted) youve got to push and pull the the door sashes into place.
Dont undo the hinge to body bolts as they will be mastic'd onto the body and it dries like cement. You dont get any real adjustment from the hinge to door fixings. other methods are putting your foot on the bottom corner of the front door, and pulling the top of the door inwards to straighten the door up, but do it gently or you can crease the door
It is a rough job, and your pride and joy, if I were you I would stick to playing with the door striker plates, you cant do much damage there! If that fails, take it to a bodyshop I'm sure they will sort it out for you,