Check my build thread and you will see what you are in for with the rear window channel.
That support in the trunk looks like factory crappy welding to me. Have seen that many times. Yours is savable but its gonna take some fab work. :D
I am following your build, while I don't have much thin metal experience I do have a fair amount of welding background and what I think is the basic amount of metal fab skill not to absolutely destroy the thing.
I am also following your situation. I am afraid that is what mine looks like under the cap, however my perches look semi ok.
I know this isn't going to be done for a while, I have already sat on it for ten years so it is what it is. I have gone back and forth on selling it and buying something built already, but I want this one to be mine not someone else's car. If it take ten more years it takes ten more years.