Fabricating patch panels is all fine and dandy until you come to a compound curve, then all hell breaks loose. I'm doing the PS fender well area right now, and can only manage to fabricate decent panels in small areas. I tried at first to tackle a larger area, but I was just going in circles. I've also been working metal for 15 years and have done MANY restorations. I haven't delved this deeply into a rust repair restoration though, so some of this stuff is new ground for me as well. I do have a suggestion on the fender arch lip re-creation. If you haven't cut and chopped yet, go out and buy a piece of 1/8x1/2 steel bar about 48 inches long. Work that to precisely re-create the arch in the fender, and then, before doing anything, cut just enough steel away in the fender arch to allow you to insert and tack in that new steel bar arch. That then defines everything moving forward and will make the end result far more precise. This is how I'm doing it.
A very good rule of thumb to work by is to never cut away more than you intend to replace in a single session. This allows you to keep fresh in your mind exactly what shape you're trying to re-create at all times. If you just remove the whole fender well or arch, you will NEVER get it back to the original shape because you've destroyed all of your guides. Methodical is key.
AND, rust repair sucks, no way around it.