First, go ahead and take out the middle bench. The ribs on your boat extend up the hull. These are sufficient for structural stability. No need to add any more "support".
Second, putting a floor in (over the ribs, either wood or aluminum) is actually support in itself. Once again, keep it simple and keep your floor low.
Third, inbetween each rib, cut out pieces of marine foam and lay them in there (May only be 1.5" or 2" thick). Once you install your floor over the ribs, you now have more "emergency foam" hidden under the floor just in case you take on water.
Fourth, 8" of freeboard on a 12' aluminum jon boat is certainly not ideal, but it isn't as worrysome as the members here make it out to be.
Take each step slowly, make sure you craft the decks to the hull, and test the boat out after each new addition is complete.
Not to disgrace any members here, but the project you have in mind is valid and can be done if you just make sure to check the boats "buoancy" after each addition. Good luck, keep us up to date.
What is your background ? What proof do you have that every thing you stated is viable ?
Experience. I've been in a 12' and a 14' modified v-hull and flat bottom jon; both with middle benches removed and full casting desks out of plywood installed. (more weight than the "removed bench")
Second, currently working on my own project with my father; jon boat to bass boat conversion. I'll post pics of the entire project when done
Just for good measure, go ahead and check out tinboats.net since you seem to be hesitant about what I've suggested. (My post is on the conservative side).
Lastly, I did say "test" the additions right? A little bit of common sense goes a long way; just be safe about it.