Body panel replacement tips/advice needed

I agree with evil 340's weld the complete seam.
I flanged the patch panel on the workbench. You probably wouldn't be able to get your flanging tool into that area near the outer wheelhouse. Flange the patch so that it slides up behind the quarter, screw it in place and weld the entire seam.
IIRC, you are getting a new tail panel from AMD? It's a nice piece but you will want to fit your tail lights before you put it on the car. You will probably have to do some trimming of the tabs that the tail light fits around.
How is that small filler piece at the lower edges of the tail panel? Mine were rusted out and I had to fabricate a set, compound curves - I think they are being repopped now? That little corner piece that attaches to the 1/4 panel, tail panel and trunk pan extension.
Put your tail panel in place and clamp or screw it to hold it, and make sure your trunk lid shuts correctly, that your 1/4's haven't moved while the tail panel was removed. When you are satisfied with the fit, weld it in. Get your tail light brackets in place where you think they go, test fit with the tail lights before welding them in place, same with the trunk latch brace.
Good luck with it. It's a challenge, but very doable. Just take your time, test fit and double check every measurement before cutting, and check again before welding.
C