Sounds like you are going to have quite a bit of metal replacement to do. Given that, I would hold off strippng all the paint until you get the heavy metal work done.
Given that the full Goodmark quarters are at least half-year out, you might want to start doing the inner fenders and rot repair up front. Then, move back to any floorpan work, and finally the trunk. The trunk is easier with the quarters cut out, but just cut the vertical portion out to start with. This will keep the car in shape while you do the trunk. Get the trunk done and the full quarters might be available by then.
I had my car blasted when I had the trunk and floors done, but the quarters were still off. I was able to get DP-40 in every nook and cranny of the trunk with the quarters off. The quarter skins are going on this week.
You might also consider getting a rotisserie to make this job easier.
Does this help?