Re: Chris craft
Interesting boat type - I don't think I've ever seen that setup before. I don't think I'd go the foam route as it will just absorb water and probably create clearance issues for your cabling, fuel line, etc.
What is making it fill with water? Is this while under way or just sitting? Is the engine significantly oversized for the boat creating a stern-low floating attitude?
Some options might be to add some more drail holes, this time just above the waterline. Cap them on the outside with those ball valves that do have some effect (not perfect, however) in keeping water backflowing. The water should then drain to the level of the new holes before you get up on plane, then hopefully drain the rest of the way once up and running.
If you do drill through your transom, use some kind of thru hull fitting and seal the exposed edges of the holes really well to prevent water seeping into the wood.
Good luck!