@Gunner90 , awesome thread so far. We're in a similar situation.
Your cost-benefit analysis is sound. Invest first in mechanical, then cosmetic. Ol' pen and paper lists have really elucidated this for me time and time again...
...but I sure want that 38g gas tank haha.
Further, please keep us in the know about what you do for the rain gutter rot.
A quality 120v MIG welder, a 4 1/2" anglegrinder, and a flap wheel will be your best friend in these trying times... and.. time to start scrounging scrap bed frames and car parts off the street to practice/offend the missus.
I'm going to likely zap my roof holes as best I can, after a few bodyshop quotes, since I have done amateur welding enough to ride my own choppers. But; as @brownbear said, quality bodyshop-quality work for rust prevention is key where the innate design of a vehicle tends to create rust for vehicles.
THAT SAID: If you wanted, this really is the time to look into an amazing custom opportunity. A pop-top could be amazing. I don't know what scrapyards are like around you, but with some fabrication skills (and I KNOW Floridians can weld and build amazing stuff)... you could have a REAL unique vehicle. Further, the aluminum pop-top pickup truck camper game is getting pretty fever pitch... you could probably find a nice one on Expedition Portal or a local craigslist, 'adapt' it, and then weld in the framework to the top of your bodywork...
...here's some nudges / inspirado:
'Mud thread with a '62 Turned Pop Top
Urza Minor Vehicles (the folks who do the Honda Element poptops)
Gearhead Junkie article reviewing pop-tops
Awww man, I'd love a pop top tent. Unfortunately the lady would end me rather quickly. So, for now, the game plan is to cut off the rain gutter and outer shell, about 2-3 inches up from the rain gutter, and replace with rust free metal. As I go, I'm planning on spaying in between the roof metals some metal prep followed by POR15 in there. Now I'm currently practicing on some scrap metal my neighbor gave me so my weld is nice and worth it. Obviously I'll paint everything afterwards to match the rest of the root beer color. Seems like this is the best way to do it