IIRC, there is play in the mounting of the doors on the A pillar both up and down and in and out. Loosen up the screws where the door bolts onto the A pillar and see if you can lift the door up and then re-tighten. I know I had to mess with that when I mounted my doors. I also had a hanging door, but it was at an angle (your's don't appear that way), and I had to shim out the bottom hinge to get things to align nicely.
The angle and gaps at the rear of the door can be tweaked by adjusting the shims where the body bolts onto the chassis at the very rear. I also messed with that a little to get the gaps at the rear of the doors looking better. Also, on the subject of the doors, I bought new latches that bolt onto the B pillars. They give you a bunch of shims to get that right, but in my case, I had one door that I had to grind the back of the latch to get the door to close properly.
Doors are alot of fastidious work, but just keep trying differnet things and you will get it them right, You aren't too far off.