When it comes to door gaps I always use the front leading edge of the rocker panel as a reference point. I line up the lower door edge corner to the rocker panel. I have also gotten into the habit of loading the door when doing this, because once the door is loaded, the weight causes the door to droop a little at the back. And you want a nice straight line along the lower leading edge of the door to.
Good luck and enjoy there fun to work on.
