I had been running an intake setup that was sealed, including filter, up all the way to a 3" hole that I had drilled below the left headlamp. These are old photos over at jeepforum:
http://www.jeepforum.com/forum/f225/homemade-custom-coldair-intake-770846/index2.html. On that page, mine is the setup with the heat-wrap and the inline filter with the red-housing. It was basically a cowl-induction type setup but it piped directly to the front grill instead of making a u turn to the cowl.
After I got a second intake manifold I had it sand-blasted, bored out to 62mm and then I mailed it out for ceramic coating work. Then I started thinking about doing something else intake-wise besides my 3" pipe/tubing straight out the front (which I suspected might have been more restrictive that I wanted, despite the cooler air it was pulling).
I looked at this old Jpmagazine piece on intake test numbers on 4.0L engines. It looked like they were getting the best torque numbers with the Airraid setup with the Synthflow filter setup (not the oil/cotton gauze deal). Looked like the Airraid tube tapered from about 2.5" at the TB clear up to 4" where it met the metal heat shield.
http://www.jpmagazine.com/techarticles/engine/154_0804_jeep_wrangler_intake_shootout/viewall.html Anyway, I bought one of those Airraid jobs for the 2.5 a while back, figuring the 4 banger was a 5/8s of a 4.0L and used the same emissions and A/F sensors and all that. So, if the Airraid worked good on a 4.0 torque-wise, it'd probably be ok on the 4Banger.
Going to install my over-invested-in intake manifold and the Airraid intake kit with the synthflow filter and see how that works. Probably not going to harm much except if I account for the damage to my bank account
But, hey, all that work on the intake manifold meant dough for dudes in the custom auto/parts service industry; so no regrets on my end.
If my Jeep saw a lot of water/mud, I'd run an ARB snorkel and maybe an Apollo filter or maybe just the stock paper and airbox, though.
