Dr. Dyno makes three strikes for a home run
The problem with the stock intake is that the front tube on the airbox is too small so that's where the main restriction lies, not in the air filter. If you go to
http://www.jeep4.0performance.4mg.com/ramair.html you'll see what I did to my stock intake many years ago. Basically I did the following:
1. Enlarged front rectangular airbox tube by 50%.
2. Inserted a K&N 33-2018 drop-in filter (flows ~450cfm as opposed to ~370cfm from a clean stock filter).
3. Removed the "trumpet" that was restricting the airflow coming out of the airbox lid.
4. Insulated the airbox with my famous foiled windshield sunshade to lower the intake air temps. This trick really did work as I found out with my digital thermometer.
This is fine as long as you have a mildly modded bolt-ons 4.0. If you start getting into porting the head and/or adding a cam, or you have a stroker, you need something better-flowing. Enter the FIPK but not K&N's expensive kit that still breathes hot underhood air. I'm referring to my expertly designed

homebrew FIPK instead. Crude but highly effective. Take a look:
http://www.jeep4.0performance.4mg.com/FIPK.html
DON'T use metal tubing for the airtube. It acts as a heat sink and raises the intake air temps. Use PVC plumbing pipe like I did instead. Oh, and you don't have to stop there. If you really want to lower intake air temps. and underhood temps., I have another trick up my sleeve. Stick an insulating blanket to the underside of the intake manifold. It really does work:
http://www.angelfire.com/my/fan/manifold.html