Hi Andrew,
First, throw the timber composite deck away and replace with 4mm ply. I did mine (now done several the same way) using the same method as Trevor but replaced it with 4mm, albeit the ply had a layer of glass on each side. The glass adds strength as one side is in compression and the other in extension (the opposite).
As for paint, not sure where this "urban myth" of auto paint has come from, but I have done all my mossies in auto with not an issue and I am talking of about 6+ boats now (counting my son's, timber and glass) .. our boats would still be some of the best looking boats on the beach, my present one in metallic and now 3 seasons old... there is always the issue of quality and application.
We have and will continue to use 2 pk Polyurethane ... but then that is what marine paint basically is, and a car sits in the weather as much as a catamaran. I would not use auto tho' on a boat that is permanently moored and sitting in a marina.
Food for thought and you get what you pay for.
David
Salpicon de Resplandor, 1744