I'm sorry dude but i don't understand your way of thinking.
"I really can't get more in it because of that weird frame piece..."
It's called the fender brace if you want the actual name and 1.) you can unbolt the bottom part very easily and bend it back or 2.) cut the thing off with a dremel. It's not like you need it any ways if you get hit in the fender your hosed anyways!
The only way you would get a huge amount of water in there on rainy days is if your one of those people that drive though flooded streets to get where you need to go.
And as for the weird sounds. You might need your head examined. Superchargers with the K&N filter on the end sound mighty mean!!!I mean who doesn't like their car to whine when they get on it when they have a supercharger ?
Just my $0.02