All the above is good advice, here is an excerpt from a thread I submitted to awhile ago...
If your hinges are in good condition life is much easier for a start. Also, it would be easier to accomplish this with the front fender off the car, I am not sure what state your car is in. Keep in mind we are aligning the door to the rocker/quarter panel, not the fender.
There are a few ways to go about this depending if the striker has been removed or adjusted out of position. If it has not been adjusted, you can latch the door closed and then loosen off the hinges at the A pillar and position the door for height and length and snug up the hinges. Now the correct order here would be to loosen the two inner upper and lower fasteners and leave them loose enough to move but so they will not allow the hinge to pull away from the A pillar during adjustment. The outer A pillar hinge bolt(s) is the one we will use for adjustment. Now I am assuming the fender is off or the splash shield is out of the way to gain access to the forward hinge bolt. Don't worry about the in/out adjustment yet, that's the last step. I use plastic fibre sticks that auto glass installers use for initial gap spacing, the are 3/16" or 5 mm in thickness which is a little tight for our MoPars but its a good starting point. Close (latch) the door, loosen off the upper and lower hinge pillar bolts and carefully insert the fibersticks at the front of the rocker and the rear close to the 1/4 panel. Now look at the door to the 1/4 pnl gap. Does it match the rocker gap? Don't be too worried about the overall height, that can be adjusted later. slide the door forward/rearward as required, then snug up the two front outer hinge bolts. Now try the door, it will probably drop a little as you open it, no worries, all you have to do is have an extra pair of hands lift slightly up on the door (while slightly open) and loosen the lower hinge outer bolt to allow the hinge to move slightly rearward. Tighten and try to close, make adjustments as necessary. Ideally at this time you should remove the striker, this will allow you to do the final adjustments without having the striker influence the fit. At this time the door should be square in the opening (rocker/1/4 pnl) but requires lateral/vertical adjustment. before proceeding, tighten the inner A pillar hinge bolts upper/lower.
Have a look at those beautiful body lines...does the door need to go up or down? Height is first here, in/out 2nd. If height adjustment is required, then all 5 (3)upper and (2)lower hinge to door bolts are loosened and adjust for height. Always use the uppermost bolt on the upper hinge as the first to be tightened, then the lower. Once height is good, loosen off only the lower hinge and swing the door into alignment with the rocker/lower body line on the 1/4, leave the lower 2 bolts on the upper hinge loose during this adjustment...once the door is aligned to the lower, snug one of the lower door hinge bolts and proceed to adjusting the upper hinge into alignment with the top of the 1/4 panel/upper body line. Of course when everything fits...tighten her all up, sit back and have a beer...This is a difficult task to accomplish and takes patience, it can take an experienced guy a fair bit of time...let me know how it goes or if I can be of more assistance.
