Ok, I will try to make a guide for setting a door. I hope this helps.
#1 You set the door to the rocker and 1/4, THEN you set the fender to the door.
Here is how things work:
The hinge bolts on the body allow some or all of these adjustments (depending on the car) forward, backward, up, down or tilt.
The hinge bolts on the door allow some or all of these adjustments (depending on the car) up, down, in, out and rotation (moving just the bottom or top in or out).
Normally, if the body hinge has not been removed, you don't need to mess with them.
First set the your basic height. This is a simple matter of having a jack under the door and tightening bolts.
Now set your basic "fit" as described below:
When adjusting the door, using the (4) door hinge bolts, work with one upper bolt and one lower bolt but have all 4 installed. 1 upper and 1 lower will be loose and 1 upper and one lower will be just snug enough to prevent the door from moving on it's own.
Note: I will often remove the striker for door adjustment. Remember, you are adjusting only to the rocker and 1/4. You are not adjusting to the striker or fender.
Adjustment using the 2 snug door bolts: This is a repetitive process so I will only give the basics of how it works.
If you need to move the bottom in/out, you loosen your 1 snug bottom bolt and shove the bottom of the door in/out, re-tighten the bolt, shut the door, hold the door closed with your hand and check panel fit.
If you are in/out on top, you loosen your 1 snug top bolt and shove the top of the door in/out, re-tighten the bolt, shut the door, hold the door closed with your hand and check panel fit.
Using this process, you can walk a door in or out and set it's angle to the 1/4 very quickly.
All of these steps may need to be repeated including going back and fine tuning the height
Now adjust your striker to the door. Your door should not move up or down when latching. One way to set the striker (old school way) is to have the striker just snug enough that it stays in position, now slam the door. that should set the striker where it naturally wants to be.
The way I do it is the carefully watch the latch and striker engage while slowly closing the door making adjustments as needed.
All of the above sounds like a bunch of work but I can normally hang and adjust a door in under 10 minutes.
If you have removed or adjusted the hinges at the body, things become more complicated but it's the same process of walking the door into position.
In my opinion, you should never use shims on a door hinge.
