Project is looking awesome! I plan a similar setup on the Squadron..
Here are a few pics of some testing on the Cobalt I just completed.
To address the functionality of the "Ram Air", Merc used it on its new 1300/1350 engine with a 50 HP gain! Apparently there is some truth to the theory...
From Mercs website;
http://mercuryracing.com/1300/
"Air Intake
The horsepower these engines boast is directly related to the way they breathe. The air induction. As is typical for most sterndrives, the 1300 breathes ambient air from the engine room. The 1350, on the other hand, breathes cooler outside air through a direct air induction system. It’s that cooler air that gives it the extra boost of 50 hp. The air induction system does require computer aided design (CAD) integration with your boat."
As for the water ingestion a little mist, rain or spray would prolly never make it through all of the ducting and in to the TB. Especially at the speeds you would be running when it is raining. Just have a low spot in the duct and a small drain hole, 1/4" or so will be plenty. Anyway, I have ran engines with water and water/methanol injection so again a little spray will not hurt a thing.
Now, if you stuff the boat and the wall of water hits the scoop that would be a different story....
And it seems you have covered the engine compartment ventilation needs as well so again, awesome project!:USA: