The art of aligning body panels....I've done a-bodies, but they're all the same. The quarters, cowl and rockers are your fixed points so you have to strike a balance to all of them. You have to start with aligning the doors to these points, because they're welded and have no adjustment.
Also remember to pick your battles. The most important gap is the rear door to quarter both from a gap and flush to quarter perspective. The gap is usually 3/16" nominal. The cowl to door alignment gap is next because that's where the best line of site is second to the door to quarter. The rocker to door gap at the bottom, is the red headed step child because if you sacrifice anywhere...that's where it happens. If I have to sacrifice there, I typically want the door to project farther out from the rocker because when you look down from a standing perspective it is less noticeable.
Step 1 is to tape the edges of both the doors (with multiple layers...3 to 4) also tape the door sill edges and the rockers. Nothing is more irritating if something slips and a paint chip occurs. At this point, the front fenders are not on the car.
Another trick is to not "tighten" everything real tight until you are happy with the gaps. A little slip with some friendly persuation can go a long way. You want it snug so it doesn't go too far, but not too tight it will never move. Also, a flat bar with a lot of duct tape plus some wood shims always help in moving things aroung while the bolts are snug but not tight.
I actually like to use some thick cardboard, or a couple layers of thin cardboard to set the rocker to door gap at the bottom. You can rest the door on the cardboard initially to get preliminary gaps set. If you need to raise or lower the door at this point, put some cardboard shims or wood shims with duct tape on them to get the front and back heights set preliminarily at this point. I like to set the top flushness to the quarter and the cowl as close as possible at this time. It's good to set the door to cowl gap close at this time also with the door about 1/32" above the quarter if there are no guts. If at a later time this needs to go down, a snug bolt with a little downward freindly persuation at the back of the door works wonders.
Once the door is on for the first time, I typically try to get the door gap at the back to look as good as possible first. That means adjusting the hinges at the kick panel area. These will allow fore to aft sliding along with height adjustment at the cowl area. Keep the cardboard or wood shims in place at the door bottom/rocker area until you are happy with the door to quarter gap.
With that done, I work on flushing up the door to the quarter so that it is flush top to bottom between the back edge of the door and the quarter. That means loosening the bolts between the door and the hinge. Just remember....what you do at the front of the door will follow suit at the back. If you move the bottom out at the hinge the bottom at the quarter will follow suit.
Worst case....and I hope this would have been done prior to paint....you can torque the door. If you are extremely dissastified with the flushness of the door to quarter vs. the door to cowl and rocker alignment, you can "bubba it" and twist things. I don't like to do that after paint.
Last thing....you are your own worst critic. When you are in the mix of doing this you are striving for perfection. Sometimes you have to step back and look at the overall picture.
Case and point.....I helped a friend do a 70 chevelle convertible who "assumed" aftermarket parts would be a perfect fit and never "dry fit" the car prior to paint. We did a lot of post paint tweaking and making the best of what we had. I thought the gaps looked like crap after about 30 man hours of tweaking, but the car was together. He drove it to work the following Monday and the "car critics" were impressed, and as I looked at it I realized it was pretty damn nice....and I'm picky.
Be paitent and careful. Once you get the first one done the second comes a lot easier. Don't be too disapointed if you need adjustments once the fenders go on....by the time you get to that point you will know what needs tweaked and it will go quick.
