Think of it this way, you have to sub-structure (frame and floor) and the super-structure (outer skins like the quarters, Dutchman panel, etc) (BTW these are my terms, not industry official terms); I would recommend you leave as much of the super structure in place as possible and repair the sub-structure at least to a point that it can take a load. The frame rails along with the trunk floor serve as the foundation for the rest, therefore you need to get that in and located, and if possible secured strongly. After that, you can build up and out (wheel houses, trunk lid hinge supports, Dutchman panel, quarters, taillight panel, trunk extensions, rear valance (fitting it).
I am pretty sure this feels a bit overwhelming (I feel overwhelmed looking at the pictures), but you have come this far and are doing an excellent job. Again, these cars were not well constructed when new, with the focus you have and the attention to detail you are applying, this car will be constructed better than when it was first built.
I am pretty adventurous when it comes to cars and the work load I would take on, but I am not sure I would have taken on this project. That said, I am very impressed with what you have done thus far and the hobby will be better because you have saved this car. Yes, it is going to absorb money like a sponge, they all do, but in the end no one will believe what you started with and what you achieved. You definitely "got this" and will forever be able to look at the car and know "I did it". Throwing a drive train into one of these along with an interior and perhaps paint is childs play compared to what you are doing, you are truly "building" a complete car. Hang in there and continue to take it slowly and methodically, it will turn out just fine.