I don't have mine sucking air from behind the fan (and I doubt the original poster does either) and pertaining to his original question, the Mass Air Flow sensor should adapt to any increase in airflow just as it would when increasing/decreasing the throttle. Also, the Intake Air Temperature sensor should compensate for the air temp changes as well. No, a "CAI" won't bring in air thats any colder than the factory - I will gladly concede that fact. However, if you look on a lot of tuning sites the airbox is left alone and the hose swapped out to something smoother like an aluminum pipe specifically shaped for the run between the airbox and the throttle body. The factory airbox is A-OK for 99.9% of people out there and the only reason you change the hose is smoother airflow, which again, won't really help powerwise a lot, but throttle response may be a bit better. If you think your off-the-line power is lacking, was it that way before you did your mod? From the handful of 4.0's I've ridden in (SOHC and OHV) they seemed pretty torquey to me - but I'm accustomed to my 3.0. Perhaps if off the line acceleration is what your looking for, a regear may be in order. I suppose its possible that when you mash it, the engine leans out slightly, but as pointed out above, the engine only sucks in as much air as its designed to and no drainage ditch monster size pipe or piece of tubing will ever change that unless you shove it in with a turbo or a supercharger. Have you done a tune up lately? A set of plugs and wires will go a lot farther than an intake kit and costs a hell of a lot less. Good luck.
P.S. - And if you want to know why I slapped a kit on it's because:
1. I broke the clips on my factory airbox (one was broke when I bought it and I broke the other one day when changing the filter)
2. Boneyard pickings are slim around here
3. God knows what a dealership would've wanted for a new one
4. I just got one of those universal kits from O'Reilleys and got the pieces to route it to behind the headlight - and yes, I have raised the hood after driving for a while and my MAF housing is still cool to the touch.
5. It was fairly inexpensive and looks a lot better than those "shower drain" mods I see in the Tech Library