Wow...I hope you have some baseline measurements to go off of. 1/16" off here means 1/8" off there and 1/4" inch off somewhere else. You definitely have your hands full, especially when it comes to all the mock up mounting you're gonna need to do. One thing you have going for you is the deck filler is still there and being its a braced panel underneath and to the rear tray, it should hold some sort of resolution as far as still being a true panel for reference. Mounting the trunk deck lid and insuring a good gap between that and the deck filler will give you about the only kind of reference you have back there.
I would start with the trunk pan, especially if it is a one piece....Make sure your rails/shackle mounts are true and weld in. Tying that in to the rails, to the back upper pan and the inner wheelhouses will at least start to firm things up a bit back there. After that your gonna need to mock up the new quarters. Put on the trunk deck lid, Check the decklid to deck filler gap is equal and make sure the gutters sit in line as well as the lip of the quarter along the deck lid. From there you should get a feel of where your tail light buckets will seat as well as the rear fill panel. Once that is mocked up, mock up the rear crossmember and insure the extension panels will fall inline. Once all mocked up I would start welding in the tail light buckets to the lower trunk gutters and then to the fill panel. After that, the fill panel to the trunk pan and rear crossmember to the trunk pan/rails. At that point the rear of the car will be pretty firmed up, but still pliable enough to make minor adjustments. I would confirm a good fit with the extensions and wheel houses, recheck the decklid fit all the way around and then check it again and then start to weld in the quarters.
Best of luck to you...That's my kind of puzzle. Heck of a challenge to say the least. Best I could come up with by looking at an 6" picture and typing about it for 5 minutes. Take your time and go into it with an organized plan of attack, modify when needed. Don't wing it. I'm sure you know, fresh tin isn't cheap. Once you start mocking up parts (#10 Sheetmetal screws work great), you're gonna start to get a feel of how you need the flow to go. Before you even dream of striking an arc (besides the trunk pan) be sure that you are lined up everywhere on all the panels. Like earlier mentioned, a little bit off here is a lot over there. Hope it goes well and holler if you need some help. Bunch of us here that have played with putting skeletons back together.