I need some thoughts as how to proceed

I just finished doing the rear frame rails on my challenger and a decent chunk of the trunk pan. Not a full rail or trunk pan replacement, but some pretty big sections. Anyway, I used a spot weld cutter to separate the rails from the floor and then replaced the rails, leaving the old sections of floor I was going to replace separated from the new rails.

I did it that way so that the original floors could help locate the new rails. The holes from the spot welds, the height of the floor, undercoating and paint lines, even rust marks, etc all give cues to the rail location. Obviously you need to take a lot of measurements still, but leaving the floors in place helps to constrain the installation so you're not just locating the rails in space. Then with the rails attached to the crossmembers I removed the sections of floor and replaced them. If your floors are totally shot that may not help you, but if they're even partially there it will make locating the new rails a little easier.