I'd plan on buying a fuel injection programmer.
The stock fueling and throttle response is hampered enough as it comes, and letting more air into the engine won't make it better without compensating for it with a programmer.
I know as I've tried it both ways.
This is like installing an aftermarket exhaust and doing airbox mods on your old carbureted street bikes without doing a jet kit.
Everybody seems to think, "Baahh, I don't need one of those things..."
Until, that is, they try one for themselves. :)
You can certainly remove the entire intake snorkel top, just be prepared for noticably more intake noise, which is the whole reason the bike comes with the Mickey Mouse intake flapper and snorkel that extends down into the airbox to begin with.
I tried it as shown in that link, with the entire top removed, but didn't like the tone of the added noise.
It wasn't the amount or volume of the noise, but the tone of how it sounded was irritating to me.
It was kinda' like having to listen to a pop song that you don't like. :)
So, I compromised by first removing the entire top as shown, drilled-out the plastic rivets on the underside of it as well (yes, there are more on the bottom side, too), and separated the part of the inlet snorkel that extends down into the airbox, which is doing much of the silencing and air restricting.
I was then left with just the upper half, minus the silly little flapper.
This was a great compromise, as the irritating pop music noise was gone, but the bike was no longer choked-up like a mouse in a trap.