I'm with huntinfool, strip it down and rebuild from the bottom up. It is also easier to make bottom repairs while it is striped if any are needed.
As far as rebuilding the decks; it looks like I would keep 'em at about the same height, making allowances for battery storage, fuel storage and maybe some dry storage. But, I am a crappie fisherman and most of my time is spent with rods in holders either straightlining or spider rig trolling, so I like a little higher sides for mounting rod holders, lantern holders and stuff. Plus I like to put my feet up while I'm seated. :mrgreen: Looks like a good platform for whatever you want to do. It will be a lot of work, but when you get done it will be a better than a production boat and be exactly how you want it.