Nice thread. I just finished reading it from start to finish. I know who much work this is as I'm doing a large job myself on my 70 Challenger. Thankfully mine does not have roof issues but everything else on my car was rusty so I've been slowly cutting and welding in new.
On your welding...I too had never used a welder until my project started. Not sure what your using but I went with a mig type with gas rather than flux core. I use small .025 wire rather than thicker stuff for better control on thin metal. I also bought a welder which automatically feeds the wire at the correct speed so I don't have to fight with it. The result? In the first 10 hours of welding, it was good but welds were not pretty and I spent a lot of time grinding. After that, I found myself getting better and better. Make sure you have a good auto darkening helmet, use bright lighting on your work to help see what you're doing, I keep the shade on my helmet around 9 so I can still see the work well. If you find the arc blowing through your work, then you are welding in very thin pitted rusted out metal or you have too much heat (current). Make sure you also weld in small increments or the heat will warp it bad.
On your rear quarters...have you inspected them well to ensure the rest of them are useable? They typically rust out down low and god only knows how much filler has been put into them given what they did to the rest of the car.
If you are certain that the only part of the quarters you need is the upper triangle at the roof, private message me and I will check mine to donate for your project. I am currently doing the metal work on the back half of my car and I plan to buy new quarters. My old quarters have rust down low but the triangle areas of mine might be useable for you. Can't promise much until I remove them but if the are good, I will take care in removing them and you can have them.