What is a Cheap alternative to Waterproof casting deck?

I may have done wrong with my aluminum boats....
When changing out transom wood which I laminated with epoxy and sealed with epoxy then installed. I sealed the motor well area to the wood with sikaflex as I felt it would allow a tad bit of freedom of movement...aluminum and wood heat and cool and swell and shrink at different speeds. I then painted over it. I have been happy with the results.

Oh...all through hull and wood holes like for the motor mounting I predrilled...used a paintbrush and epoxy sealed them too....when I installed the part or bolt I additionally used 3m 5300 marine adhesive sealant to grant me just a bit more protection as I hate leaks and positively loath soggy rotten wood. Has worked well for almost 10 yrs on my Jon boat and 7 or so on my starcraft aluminum converted to cc.
Your mileage may vary

Don't follow my example unless someone with more experience here says it is good .

 

I will be using that marine sealant but it's the top I'm not sure how I will be getting the transom out yet either grind or bend the steel up it is sealed in pretty good

 

I'm always thinking about my boat and how to improve it a bit whenever I get around to doing things...my hornet has the plywood and carpeted decks which i feel is not ideal when it gets wet, cos it takes a while to dry and I think the ply may start to rot away eventually, any ideas, maybe alloy or a plastic type of product.?

 

A cheap way to waterproof ply is to use Titebond 3. It is a wood glue but fully waterproof even for constant exposure to water. You can also use it to laminate a layer of cloth over the ply. You can seal leaks with self adhesive flashing intended for buildings. Heat it with a heat gun in position and it's going nowhere in a hurry. You need it cheap? Ask me!