Good luck, I suspect you'll be surprised at how much a shop will charge to attempt this, if any will even consider it.
The foam that has become waterlogged, is no longer doing what it's intended to do: In a whaler, that's fully support the deck & hull, and provide flotation.
Search thru the forum, there are a few Topics about this. There is plywood backers behind some of the stuff attached to the deck, the center console for 1. That plywood is likely compromised as mentioned and the transom as well.....
Good luck w/ your project
Boat & boat resto safely