If you want to raise the deck above the water level, one way is to make the deck and boat lighter. Plywood would be the worst option there.
Chaser did a foam core deck and nicely offset the weight of a heavy Honda 135. He might have even raised the boat in the water after adding perhaps 100 lb of outboard.
Decks on early boats have end grain balsa core. I think it is a spiritual cousin to an *engineered* foam core deck.
In my opinion, I would do an engineered foam core deck, followed in preference by balsa, and avoid plywood due to weight and water migration in plywood (balsa on the end grain is somewhat better).
Then I would move the console and batteries forward, (and possibly the tank) and you can maintain the CG and lift the boat out of the water, make it plane better and float better and use less fuel.
If, after all that, you decide you still want to lift the deck, then I would cut the tops of the box stringers, replace the floatation foam, and raise the height and volume of the foam, and install the new deck. And I like the idea of two smaller *ethanol resistant* plastic tanks so you don't have the free surface effect of fuel sloshing fore- aft in a long skinny tank. And you can tune CG on the fly by draining from one tank or the other.
Older Seacrafts are sorely lacking in floatation foam. So they can sink. Quickly. I am a big fan of a bit more foam in the hull.
I have done H80 foam cored fuel hatches and bulkheads for the 25 and they are very stiff, strong and light.
[edit] Here is Chaser's thread: He took a beating early on about a heavy motor, but walked the talk with a foam core deck and heavyish 4 stroke and the combination seems to work well.
http://www.classicseacraft.com/commu...ad.php?t=26989