I just read through your project. I've been repairing boats for a bit over 11 years now. Here are my thoughts.
Bracing: What you did should be fine. If it was me though, I would bolt some blocks to the outside, through the rivet holes, amd use ratchet straps. You can adjust them easier if needed, I think it would be more secure.
Floor and Stringers: Hopefully you can still see the old floor line on the hull. Make your stringers a bit taller than that, set them in the same places, and trim them down later. It's so much easier than cutting too short and having to work around that. Youll need some boards screwed across the tops to keep them in place, set them in with thickened resin, and will be glassing along the sides to attach them to the hull. Do the entire stringers, floor, and might as well do the transome too.
Foam: Take it all out, it will at best be in the way. Use a reciprocating saw to cut into squares, then a flat bar to pry it up in big chuncks. Quick, easy, and clean. New foam should be poured in after the floor is done.
The Cap: Don't do all of that mixing and matching with bottles and extruded poly foam. Some two part or spray cans when everything else is done will be fine. In this case, maybe spray cans. The two part might be a bit messy for that job. If the wood on the rear needs replaced, don't go side to side. You need those open areas to glass to. You can add small plywood blocks to support deck hardware now too.
At the beginning of this, you said you didn't care about time or money, you wanted it right. It's definitely going to be a lot of time and money to get it there, but don't skimp out.
I'll add more detailed responses as the project goes.
