Nothing adds to "detail" on a car more than nice fitting panels. If the car is a light color it is even more important. Those "black lines" that are the gaps between panels really look bad if they are not a consistent width. While using this guide and aligning your panels be sure that you open and close the moving ones very carefully after a change. You can loose the gap fast which will allow the panels to hit, so be careful.
I have to start with this very important point. ALWAYS have the car sitting on it's wheels or at the very least the weight of the car should be on the axles. That being if you want it on jack stands to raise the car up and give you more access to the bolts and such, place the stands under the control arms as and rear axle. They should be out as far as possible towards the wheels. This can still cause problems on the front. Even in a little from where the tire actually holds the car up can change the amount of pressure being exerted on the car's body. A car can be twisted or bent more than you can imagine up on jack stands when the stands are set on the frame allowing the weight to hang off the ends. This is VERY, VERY important. Of course this goes for anytime a panel is being fit, either welded or bolted on.
Hood alignment: Let's start with raising and lowering the rear of the hood. If the car you are working on has a hinge that sits on top of the cowl, your only options are to shim or bend the hinge. Bending the hinge slightly is one way to move it. If you need to come up in the rear you can put a small block of wood or other item on the hinge, to bend it. When you close the hood down (NOT ALL THE WAY) it will get in the way of the hood closing and bend the rear or the hinge up. If you need to bend it down, the only option may be to remove it and bend it a little. You can also shim the bolts between the hood and the hinge, more on this later. If you have a hood where the hinge mounts on the side of the fender or the side of the cowl like with an older car or truck, you want to "rotate" the hinge on the fender. Just pushing the hinge up and down will give you very little movement on the top of the hood. This is the strange little trick that you have to remember, if you raise the back of the hood on the hinge or raise the back of the hinge on the fender the hood will go up. If you raise the "front" of the back of the hood ON THE HINGE or the hinge to the fender it will go down. What you have to remember is you are working with a pivot point in the hinge, not a stationary part. If you loosen the FRONT bolt on the hood (where it bolts to the hinge) and put a shim, or washer between the hood and hinge, this will LOWER the hood on that side. If you put that same washer under the rear bolt it will RAISE the rear of the hood on that side. So, if you loosen the bolts from the hinge to fender and close the hood, the hinge will rotate on down in the front right? This will raise the REAR of the hood like putting a shim in the back bolt between the hinge and hood! What you need to do to lower the back the hood is to loosen the bolts (only slightly) and PUSH UP on the front of the hood. This rotates the hinges back, thus raising the front of the hinge and lowering the hood in the back. If the hinges are warn out it won't change how high the hood sits when the wear, not by more than a fraction of an inch. And I have never seen a car with these style hinges that you couldn't put the hood a half inch LOWER than the fenders if you wanted to. The adjustment is HUGE on these cars. That is one of the things that is easy to do on them is align panels.
I recommend you remove the striker or latch from the hood so that you can move it up and down without worrying about the latch grabbing the hood. After you have aligned the hood, take a piece of dumb-dumb or clay or something similar and put it on the latch. This way you can see exactly where it hits when you do install the latch. You bring the hood down till you just tap this dumb-dumb but DON'T LATCH IT. Just so the hood makes an indentation in the clay/dumb-dumb. This tells you where you have to move the latch. I do this at work everyday, by myself so if you can't get help this is the trick. Always leave one bolt on the hinge tight. If you want to rotate it back, leave the front bolt tight. If you want to rotate it forward, leave the rear bolt tight. When you move the hood forward or back on the hinge, leave the bolts snug enough that you have to tap on the edge of the hood to get it to move. Or if it needs to go back, leave the bolts a little snug, and wiggle the hood up and down and the weight of the hood will make it slide down. Remember it only needs a 1/16" or so to make a 3/16" or more change at the front. To pull the hood forward on the hinge loosen them so they are still a little snug so you have to pull up on the back of the hood to make it slide that little bit. If you loosen it up so it moves anywhere you want it, YOU WILL NEVER KNOW HOW MUCH YOU MOVED IT AND YOU WILL MOVE IT TOO MUCH, GUARANTEED. Get the hood laying flat first, then move the hood forward or back on each side to make the hood fit the hole between the fenders. If the gap is large on the front right and small on the front left, then the hood needs to me moved back on the right side. As you move the hood back on a side it will close up the gap in the front of that side and open it at the rear of that side. You may need to move fenders too. Just do each change slowly, move it VERY LITTLE. Look at the bolt and washer as you move the panel, you will see where the washer used to be, the amount is much easier to control if you watch the washer movement. If you need to move the hood up or down at the front, you have a few ways to do it. First, on each side there are the "bumpers". The hood bumpers are located at each front corner and look like a bolt with a rubber pad on top. Just unlock the jam nut and raise or lower the "bolt" so it holds the hood at the height you need to match the fender. You may find that the hood won't go low enough even with the bumper down far enough. The latch may not be down far enough. When you close the hood, you shouldn't be able to pull up on the hood or push it down. The latch should be tight enough to hold it against the bumpers tight, but not too tight. If you have to apply too much force to open the hood or it opens with a loud POP, the latch is probably too tight. If it is at the right height but you can lift it up some, then the latch needs to be moved down.
Doors: If the doors are off the car, bolt the hinges to the door and the cowl in the middle of the movement allowed. Let's face it, it "shouldn't" be too far off the center of holes. If the doors are on or if after putting them on things are way out of whack, raise the door up on the hinges as far as it will go while still staying about the right height. You always want to start high, it is much easier to come down than go up. Besides this is the ONLY time you will loosen all the bolts on the door. I don't mean ALL the bolts, leave the hinge to cowl (or center post on a four door) tight. Only loosen the door to hinge bolts. Unless it is WAY down then you may need to move the hinges up too. But do one at a time, both door to hinge or both hinge to cowl/center post.
While moving the hinges aligning the door NEVER loosen all the bolts on the hinge, NEVER. Loosen all but one, just till it is still a little looser than "snug". Leave that last on just a little snug. Let's say the door fits well but is a little too far rearward. NEVER loosen top and bottom hinges and move it forward. Loosen the top hinge to cowl/center post as described above and lift the rear of the door, a LITTLE. This will push the upper hinge forward. Now TIGHTEN that one bolt that was left snug. Do the same on the lower hinge, pushing down, but remember the weight of the door is helping, so little push is needed. Many times no pushing at all, just the weight of the door will do.
If the door fits well but is out at the top or the bottom, again, loosen ONE hinge to DOOR in the manner described and push it out or in. If it is out or in at the top rear for instance, move the bottom front in the opposite direction. This will pivot the door on the striker, and move the rear top where you want. Moving the bottom rear takes moving the top front of course.
You may need to twist the door. If the front fits well and rear is out at the top (or bottom, just reverse) you can put a block of wood at the rear of the door at the top lets say and push in on the bottom to twist the door. Some will take a LOT of force to bend, and be VERY careful not to let your fingers hang around the outside of the door edge!! I lost a finger nail doing this on a '69 Shelby GT500 convertible once (remember it well) when the block of wood fell out with all my weight on the door while twisting!!
Tip: If you are hanging the door and you have access to the hinges (either through the wheel well with the skirt off or if the fender it's self is off) you can simply hold the door up to the opening and push the latch shut. Then put the bolts in the hinge. I can often install doors all by my self in this way.
Deck lid: The trunk lid is pretty much like the hood but the hinges don't move at all on the body (usually). So shimming and twisting are a few of your only options beyond the movement in the slotted holes on the hinge. Bending the hinge or pushing up or down on the sides of the quarters, front or rear panel are the others. These should be done ONLY after all other things are tried.
Fenders: Most of the tips for doors and the hood work here, with a little twist or two. Start with fitting the rear top of the fender. I like to put all the bolts in, loose. Not falling out loose, just so the fender would easily move. Close the door, and with the hood open adjust the gap at the top of the rear of the fender to door. After you tighten other bolts this cannot be modified so, do it first. Tighten the bolt under the hood closest to the door to secure the position. You may need to shim a bolt at the rear of the fender to the cowl, to move the fender forward or back. After you have that bolt tight and the gap is to your liking open the door and tighten the rear fender bolt that is at the top of the fender in the door jamb. Now do the bottom bolt, with the door closed, adjust your gap. You may need to wedge a flat blade screwdriver or body spoon to "force" the fender forward to get the desired gap. Or just the opposite, use a 2x4 or something similar off the front tire to force the fender back to get the gap. This is one of the hard spots to get nice because you have to get both the gap and the in and out of the fender to door at the same time with the same bolt. Some cars have two bolts that are far enough apart to get the gap and tighten the front bolt and then pull the fender in or out and tighten the rear bolt to get the flush fit of the panels.
General tips: Bending a panel or adjacent panel is sometimes required. You can get this done in a number of ways, one is to use a block of wood. Let's say that along the edge of the hood there is a spot that is high. Well you can't adjust it down, the front and the rear are perfect. So you can lay a block of wood on the spot, right at the edge where it is strong. Using a big hammer (the bigger the better, trying to make a small hammer do the job can cause a lot of damage) hold the block and strike it nice and solid. Then check the results, you may need many strikes to do it. In doing this you may want to support the hood at the front with a block of wood under the hood. This way the hood is up off the fender and it will bend easier because of the solid rest it has. You can also put the block under the edge of the hood at a low spot and with steady pressure bend it down at a point if you need it.
If you are working with very tight tolerances, you can actually grind the edge of a panel or jamb to get an extra fraction of an inch. Be VERY careful and using a fine disk like 80 or 120 take a LITTLE off. You don't want to grind the metal thin of course but a LITTLE can make a big difference when you are fighting for fractions. Now, you really won't be cutting too much metal, you are really just cleaning off ALL the primer and paint there. Then when you prime it, don't put a lot or sand it thin so there will be very little on the edge.
You may want to paint the hinge with a little contrasting paint. Do it with the hinge bolted on, right over the bolts. This way you can see easier how much you have moved it.
These directions are for doors where the hinge bolts flat to the side of the cowl and then flat to the front of the door. There are of course many ways the hinges can be mounted on cars. If yours are different than you need to use the "concepts" that I have described here. If for instance you have a 1950 Chevy pickup. The hinge bolts flat to the back of the cowl but will work the same way. The door hinge bolts flat to the side of the door. In this case you do just the opposite as I earlier described. You would loosen the hinge to cowl bolts to move the door in and out and the hinge to door bolts to move it back or forward. If you find that your car has a design that hasn't been addressed, take a good hard look at your hinge arrangement. If the door is open, close it enough while you can still see the hinges and imagine what direction will it go if you loosen a particular set of bolts. Get an idea of how you can move it, then start the alignment process. These are just ideas that I have used over the years and some may work for you some won't, but it is a start. Above all, have fun!