Anyone who has been around bodywork and painting for any length of time knows all too well that paint not only won't hide bodywork imperfections, it will mercilessly reveal and enhance them-thus, the saying that paint is only as good as the bodywork underneath it. It could be said that a great paintjob is as much defined by what isn't seen as by what is seen.
But perfectly smooth, flawless paint by itself isn't enough to win awards. Have you ever seen a car with great looking paint, but with body panels that just didn't seem to fit right? The gap around the hood might be inconsistent. A door doesn't close completely flush with the quarter. Maybe the trunk lid is even with the quarter on one side but not the other. Perhaps the most noticeable flaws are bodylines that run the length of the car that change from one panel to the next. Unfortunately, our eyes are all too often drawn to imperfections and inconsistencies, and soon we can't see the forest for the trees. In other words, we don't tend to notice how well body panels fit together unless there's something inconsistent or out of place.
Aligning "hinge-able" panels...
Aligning "hinge-able" panels like the trunk lid needs to be done with the weatherstripping in place. Since the trunk seal glues on and you don't want to install it permanently yet, you'll need to tape it in place. But you can't let the tape adhesive touch the seal because it will pull off the adhesive coating. Wrap the tape around the seal outside in and then use a second piece to hold it to the car.
Of course it's no surprise that 30-40 years of use-and all too often abuse-have just torqued these cars out of shape. Not to mention what can happen with careless collision repairs or hacked-up backyard rust repair. Never mind the fact that, dare I say it, a lot of them came out of the factory that way.
Perhaps where owners get tripped up with this issue is that most don't realize just how much a car body can flex during use. Some Hemi-powered race cars would twist so much that they would break the windshield and, after a while, the door would become hard to open. OK, that's an extreme example, but it would be smart not to assume that your car is perfectly square, and even smarter not to wait until the car is painted to align everything.
Just like great paint can only follow great bodywork, perfect panel alignment can only follow expert metal work, which means assembling and checking the sheetmetal on the car before it's too late to do anything about ill-fitting parts. The guys at Muscle Car Restorations in Chippewa Falls, Wisconsin, take the time to mock up each panel on a given car after the major metal work is finished but before the body is ready for paint. That way, the panel fit and alignment can be fine tuned. Once everything fits correctly, the car can come apart for the rest of the restoration and finish work, knowing that it will go back together fitting perfectly.

The seal should be a little...

The seal should be a little long, so expect to trim it as needed.

Install everything just like...

Install everything just like you will when the car is finished. Don't skip installing the trunk springs, as they can influence how the trunk lid fits.

Start by adjusting the hinge...

Start by adjusting the hinge bolts. They provide fore and aft adjustment and some up and down movement.

These shots clearly show the...

These shots clearly show the difference between the left and right side seam gaps.

There's no factory provision...

There's no factory provision for side-to-side adjustment so you'll need to gently tweak the hinges.

Notice how the gap spreads...

Notice how the gap spreads just as it reaches the end of the quarter. This is not uncommon but can be easily fixed at this point with normal body/metal work techniques. Imagine if you found this after the car was painted!

The new trunk seal will not...

The new trunk seal will not be the same thickness and density of the old one, so a high decklid is common. There is some up and down adjustment in the hinges...

but often gently massaging...

but often gently massaging the lip where the seal mounts is necessary to bring the lid down into place.

Don't assume that your trunk...

Don't assume that your trunk lid is perfect. This one needed a corner to be tweaked just a little. Spread the force with a block, or you risk denting the metal.

Notice how the gap gets narrower...

Notice how the gap gets narrower toward the back of the car? In this case, the quarters needed to be moved out a little.

Gently "persuade" the opening...

Gently "persuade" the opening to get larger, but don't open it too far.

If your trunk lid has a dip...

If your trunk lid has a dip to it, pressing down on it with some rags placed on top of the quarter can alter the contour of the trunk lid some.

While there is some adjustment...

While there is some adjustment to be had with the trunk latch, limit it to closing height only. Don't try to adjust side to side with the latch.

When it comes to hanging the...

When it comes to hanging the doors, be sure to install all of the hinge bolts. The hinges allow ample adjustments in any way you need. MCR recommends setting the overall height, front and rear first, then side to side twist or rotation, and, finally, the in and out position.

It's also important to fit...

It's also important to fit the door to the quarter and the rocker panel first and then to the A-pillar. You'll likely not get it just right the first time, so plan to run through these adjustments as many times as needed to dial everything in.

Your first goal is to get...

Your first goal is to get the door aligned with the front edge of the rear quarter...

...and the top of the rocker...

...and the top of the rocker panel.

Hopefully the door to A-pillar/cowl...

Hopefully the door to A-pillar/cowl seam comes into place at the same time. Expect a lot of minor tweaking, as making a change in one direction always changes something else at the same time.

Of course this isn't a standard...

Of course this isn't a standard adjustment, but most doors will take a little twist if necessary. Later cars with the safety beams are not as susceptible to this move.

Like the decklid latch, the...

Like the decklid latch, the door striker should only be used to set the closing depth of the door. Do not attempt to use this to adjust the door height. Of course, all the while you're working with each door, you need to pay attention to the door-to-quarter and door-to-rocker gaps. Just realize that you may not be able to get them perfect without additional bodywork. That's why we're mocking up the car in the first place.

There are several attachment...

There are several attachment points for the fenders...

...so a good supply of various-sized...

...so a good supply of various-sized shims will be worth having around before you start.

This spot where the front...

This spot where the front of the door, the cowl, and the rear of the fender come together is one of the more critical and difficult areas to get right.

The height of the fender is...

The height of the fender is adjusted by shims that rest on an extension of the cowl.

Not only must panel gaps be...

Not only must panel gaps be even, the panels themselves must be straight. The top of this fender has quite a dip in it that will have to be hammered up to match the door and the edge of the cowl panel. Again, imagine finding this after the paintwork is finished.

A straight edge across the...

A straight edge across the bottom of the fender shows that it needs to come out some to match the rocker panel.

The fender can likely be fixed...

The fender can likely be fixed with a shim change, but if the corner of the door or fender curls in like ours, it will require some hammer work.

The last panel to be fitted...

The last panel to be fitted is always the hood. A stock steel hood is fitted much the same way as the trunk lid, but this car has a fiberglass piece that needs a few extra steps.

The basic hood-to-fender gap...

The basic hood-to-fender gap is easily set...

...by the slotted holes at...

...by the slotted holes at the nose of the fender.

These small rubber stoppers...

These small rubber stoppers set the height of the hood.

Fiberglass hoods are notorious...

Fiberglass hoods are notorious for uneven gaps, but...

...fortunately, they are easier...

...fortunately, they are easier to fix than steel ones by sanding and/or using filler on the edges.