Look at the car you are going to rebuild. If everything fits great, drill two 1/8 inch holes in the fenders one forward and one in the back. When you go to rebuild your car after all the body work is done, all you have to do is stick a 1/8th inch drill bit in each hole and everything lines up just as it was in the beginning. If your panels are not aligned in the beginning, line them up and drill holes. This is an especially good tip to use on hinges for the hood and deck lid. Door hinges are hardened and do not lend themselves to this trick. On door hinges, simply use a wooden paint stick to set the gaps.
Another tip is to count the shims and their sizes when you disassemble a car. Write these numbers and locations on a sheet of paper and tape it to the glass on the car’s interior. At least put it where it won’t get painted or lost. When you rebuild the vehicle, replace the old shims with new ones of the same size in the same location.
Another tip is to realize that body putty (Bondo) shrinks. If you work a car today with the body putty, and let it sit for a week or so, it will not be as smooth as the day you sanded it. It will end up with small ripples and waves in it. I generally do all the work, then spray the car with the primers and lets it sit as long as possible off to one side. Then come back in a week or so and smooth out the guide coat. If necessary, i may have to add another layer of primer surfacer and treat it as a guide coat layer