I'm confused. You want to keep the intake box? Or you want to keep the plenum box?
The plenum box is attached right at the throttle body and has "4.7L" written on it. The AFE Stage 2 kit (http://www.autoanything.com/air-filt...0A2601488.aspx
) removes the filter box and replaces it with theirs but attaches direct to the plenum box. You're not doing any more good with that type of kit than by simply replacing the stock air filter with a K&N or AFE. The plenum box has baffles in it and causes turbulence. It also drastically quiets down the intake. In other words....reduces maximum HP gains from an intake kit. I bought this kit a while ago thinking it would replace the entire stock intake but immediately took it out, so I have some personal experience here.
In my opinion, if you're going to spend $250 on this kind of kit, your're wasting your money. Buy the K&N FIPK and get rid of that plenum box. Or spend $30 on an aftermarket filter for the stock setup.
Simply replacing the intake tube won't do any good either. All of the aftermarket pieces as a whole make the gains you're after.
Hope that helps.