Go ahead and gut. I know those things mean well but all they are is a restriction. Even if you don't gain much you'll be better off than before. I forgot who said it....might have been Ed....but I'll quote it as best as possible. "If a landmine exloded in a puddle directly under your car on full load on a dyno I still don't think enough water would get past the intake to do any damage" While your there gutting the things take a look at Andris Skulte's page to do a free ram air mod.
http://www.skulte.com