I recently completed a hinge replacement on a 69 drivers door. What a friggen horror show! Myself and two friends did the final alignment, it took 4 hours on two separate days for 8 hours total! Don't bother measuring, what are you going to do with the numbers? As suggested by the guys, check for frame issues to the extent of a break or major fault. I would take pictures of all the gaps, doors, hood, deck lid, on flat pavement after you bounce the car to settle it. Then take floor jacks and start lifting it in various combinations. taking the same pictures after each lift and take pictures of the jack locations. Next study the pictures to see if one jack location has a greater effect on gap alignment than the others. This may zero you in on a weak spot, or it may not.
The common problem with aligning doors on a 69/70 is the interior rubber door parts and steel strip will prevent you from getting the door aligned. Remove all of it. I had to hammer the pinch weld a bit near the door light switch to get enough clearance. Take off the fender of course and replace the pins in both hinges, they sell a kit. I bought a shim kit at harbor freight and trimmed off the tabs and used them to get my alignment by shimming the hinges on the door. A 1/32 shim at the hinge area moves the door 1 inch or so 4 feet away at the latch, it's nuts. When the door is flush at the 4 points, 2 at the rocker and 2 at front and rear upper door, mock up the fender and check to make sure it is on the same plane as the door. Good luck, I pity you because it is going to be a real PITA! When you get frustrated walk away and come back fresh. You will learn a lot when you are done, and if you don't do it right the car will forever look like a hack job no matter how mice the paint and body work turn out.
