Hi Scott, and welcome to the forum!
The rear of our '64s is a problem in that the water seeps into the floor, but It's more from the frame than from the hatch. You should put a good bead of Vulkem at the frame to shell junction to stop water from getting in there. On my safari the rear of the shell didn't cover the plywood edge at the back all of the way down. It only covered about half of it. When you take the bumper cover and belt trim off of the rear end you may find the same thing. I will probably be re-engineering the cover for the rear hatch on mine. It's a hard thing to seal, with the way they built it. If you can't make the changes to the rear end you should go to lengths to waterproof your new flooring material. That doesn't mean you should use plastic or metal. It lasted 45 years with totally unprotected wood anyway. I used water-based wood floor finish on the bottom, and Kilz primer and exterior latex housepaint on the edges and in a few inches on the top surface. This, in addition to the better sealing of obvious leak-prone areas, will increase the life of my floor greatly.
There are a few good seam sealers out there. I rely on parbond for exterior seam sealing. It comes in an aluminum color. If you have panels removed, you should use Vulkem when you reattach them to each other. It's harder to use, but it's great stuff for this application. The Parbond is easier to fill existing seams with, as it's not as stiff. Check out Vintagetrailersupply.com and if you're not sure if you have the right things call them & tell them what you are doing. They are very helpful.
Also check out Prodex insulation at insulation4less.com . I just reinsulated with this stuff, and it's great to work with. No fiberglass mouse house anymore! It made a big difference in the insulation effectiveness. I heard about this from Uwe at Area63productions.com. He's a master. Check out his work if you have a chance.
I'm going to give it the ultimate test in two days, at Burningman. Last year it was 107 degrees when I arrived. We'll have to wait and see what it's like this year!
Good luck with your project.