Didn't see this one before--watching now--lots of good visual cues and I'll be making similar repairs in the trunk on my '72 Scamp. I am of similar mind with your methodology...not a concourse, so patch panels will play a part in addition to standard replacement panels and I'm not super concered about how the trunk floor or floor pans look as long as they're in there, secure, and don't leak.
I do need to replace my right side front floorpan again...the first time I did it, it was FAR from correctly done due to a lack of proper tools. Now I have a shop, a 60 gal compressor, a 140A MIG welder, and more hand/power tools...(Eastwood will probably get more of my money for fab tools).
I'm glad you took a pic of your wheels with the spacer-I'm likely to go the same route because I have an extra set of Bullitt wheels from all my Mustang bits and pieces.