A friend of mine did a '62 Plymouth. It was featured in Mopar Collector's Guide about 12 years ago. It started out as a mint, low mileage, beige four door sedan. It is now a red, two door sedan, built for Nostalgia Super Stock. He had the four door, but hated the fact that it was a four door. He also had a two door sedan body that someone sandblasted, but got a little over zealous, and warped the roof real bad.
One night, while sitting in the shop, he really started looking at the two cars, and realized that it would be relatively easy to do. He pulled both doors off one side of the four door, and the door, and inside panel from the backseat area of the two door. That was when he discovered that the inner structure of the two door is actually identically the same as a four door. It just has an extra structure welded into it, for the quarter window. The jamb for the back door is even in the two door body, that's what the factory fit the two door inner structure into. Then it's hidden by the outer quarter panel, and the inside panel, next to the back seat.
At that point, it was the point of no return. Cutting out the four door B-pillar. Once the pillar was gone, he bolted the door from the two door in, and took measurements. He carefully cut the inner structure, b-pillar, and door jamb from the two door, mock-up fit it into the four door body, and every thing lined up perfect. He welded it in, and it worked. Then it was just a matter of cutting the outer quarter panel section from the two door, and mating that to the four door quarter. Then repeat on the other side.
The best way to do this job is to have both cars right next to each other, so you can take measurements from both cars, and to facilitate the parts swap. Also, by starting out with a nice four door, it eliminated having to do a lot of body work.