I can't respond very well not knowing what sections you're talking about.....Frame rails have been swapped out, but with much difficulty....usually in separate pieces such as the rear starting over the axle housing......
If you're sectioning, it will be easier and more apt to be aligned properly IF you do one surgery at a time.....ie. remove one rear section, leaving as much of the existing steel in place as possible, then weld in the new rail at critical points, leaving the trunk floors detached.....follow with the other side, then move on to other rusted sections........but again, it's all conjecture on my part since I don't know exactly what you're up to.........
Replacing framing on the unibody is a tricky business to say the least. 8)