The XJ design is a little differnt then the YJ. Mine has a little bar welded to the bottom that slides into the cable guides for the throttle cable. My K&N was bigger then the Rocket filter and mine rubbed the bottom of the hood too. After a while the heat from the engine will cause the rubber on the filter to mold into place just fine. It might rub some of the paint away, and if that is a big deal, just put some tape under the hood. The only thing I can think of to make the tube fit a little better would be to flatten it out where it crosses the valve cover.
Paul is right, it is not a cold air intake, and thats why thay call it a "Rock-it Tube." The power comes from the larger volume of air flow, not the desnser cooler air. If it was a true cold air intake it would boost power by about 20 HP and this one claims 12 HP (
). K&N and Air Raid both make filters with a tube and a heat shield, but they cost over $250.
If the fit isn't right, call Rock-it. It has been a few years since I called them, but they were very helpfull when I bought my bigger throttle body.