You do not want to seal that part of the engine from the atmosphere.
I have a different induction system, 4 Weber IDA's but have a similar issue with keeping out water.
What I did was take a piece of 1/4" plexiglass and bend it down with a heat gun.
It covers the top of the exposed velocity stacks and does not seal against the deck lid. It is open on the bottom and is really just a canopy.
You can see through it, keeps the water out from washing with a garden hose, and opens with the decklid so it doesn't hinder access to the carbs, linkage, etc.
The stacks are 5" tall and the openings are close to the roof. The system isn't water proof but it certainly removes the majority of the concern of the engine swallowing a big gulp of non-compressible water.
The aluminum plates that you see on the carbs do the same thing to cover the screens over the jets. So far, so good.
Of course in my case, I have rear louvres, which are functional to the induction, and the sugar scoop is also since it redirects air downward towards the velocity stacks. There is no louvre slat directly under the roof scoop.
If you look at the combination you might see that there is method to the madness here?
Here's a picture.
You might be able to take the thought and extrapolate it towards a solution for yours?
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