Take a look up towards the top of this thread and you will see how severely my son and I cut up the back end of his Dart Sport to do a lot of what you are considering doing. His was eaten up pretty badly with rust, and it seemed a lot easier and more efficient to do it that way instead of a bunch of little patches and fabrications to remove the rot. Keep this in mind, that was the first time ever that either of us had done body work.
It may look like a daunting task, but once we had a plan in mind and got started on the surgery, it really wasn't that bad. All I can say is measure, measure, measure some more, then measure again, before you cut anything.
Remember, these cars were built with unibody construction - the body skin is welded to the framework - unlike other vehicles that have bodies you can lift off the frame independently. For the most part, it is self-supporting, and you would have to do some serious metal removal in large chunks to leave enough voids to allow the movement you are concerned with.
The two frame rails sticking out the back of the Dart in that one picture shows you how much can be removed and still have good support. Yes, the rails did have some flex in them, but a few self-tapping sheet metal screws were all it took to hold them in place for welding the replacement trunk back on. We grafted the back end of a '76 Duster onto the '74 Dart Sport, and I was amazed how well the drilled out spot welds from each vehicle lined up precisely onto the other. That helped a lot in getting everything located back in the right spot. Of course, if you use new replacement sheet metal, you won't have the advantage of the spot welds.
The best advice I can give you is to map out a solid plan on what you want to fix and how you can propose to do it. Think out every step in detail, use felt tip markers to sketch out the cuts, check for obstructions underneath, make sure cuts are made in good solid metal to remove all the cancerous rust, and focus on one area at a time.
See, that doesn't sound so bad, does it?
Jerry