QUOTE: "I know the 2 doors door is longer than the 4 door. What I'm thinking is the front of the roof from a 2 door could be cut off at the windshield header back to where the targa bar is. The side rails would be shortened by the difference in size between the 2 door and 4 door doors. This assembly would be welded onto a similar cut off on the 4 door."
You may be making it harder than it needs to be. The soft top roof opening is a recessed section that allows the door to seal on the same mating surface configuration as the 2dr hardtop. Why not cut the roof of the 4 dr inside the door gasket mating surface, dropping in the roof section, and welding it in without disturbing the door mating surfaces. The open area would extend slightly into the rear seat area, but you would not have to shorten the side rails or the flip top hardware. The section added to the 4 dr would have to include the latches and seal area for the top header.