You have to find and record reference points for every axis. No floor surface will be flat or level, you have to build supports to be level and they have to remain in the same place the entire time. Ideally this should be done under the original frame so that once the rear section has been removed the new one can rest on those supports. If you have to weld some braces in before removing the body because the rail is rusted in two, then do so.
And if it were me I would try to get the two to fit so that the ends of the inner and outer rails are staggered and the top and bottom of the inner and outer rails overlap like the factory did it, then butt weld the vertical ends. After the butt welds were done I would plate over them for added rigidity. I would find good reference points on both sides to cut the front section to the same length on both sides, then trim the rear section a little at a time to get an exact fit. It can be done but take your time and double check measurements as you go. Also take your time with the welding, use plenty of tack welds and use small stitch welds working from side to side so you don't warp the frame.
And if it were me I would try to get the two to fit so that the ends of the inner and outer rails are staggered and the top and bottom of the inner and outer rails overlap like the factory did it, then butt weld the vertical ends. After the butt welds were done I would plate over them for added rigidity. I would find good reference points on both sides to cut the front section to the same length on both sides, then trim the rear section a little at a time to get an exact fit. It can be done but take your time and double check measurements as you go. Also take your time with the welding, use plenty of tack welds and use small stitch welds working from side to side so you don't warp the frame.