The drop-in K&N's don't give the power and mpg improvements that a good airtube and conical K&N will. I used a stock airtube from a 4.0L TJ and added a conical K&N to the end.
I know for sure that there is more lower end torque with the stock airbox then when I was running a CAI with a K&N. I switched to the CIA then switched back to the airbox years later. The difference was pretty noticeable. On the flip side, I believe the engine had a bit more HP on the top end. Also, seeing how poorly some paper filters are made, a rechargeable filter should make a difference. My paper element had around 1/4-1/2" of extra rubber flashing around the perimeter of the filter. Depending on placement, a open element filter can end up sucking in less dense air then the stock airbox as well. It's better to grab air of possible, infront of teh radiator and not at the back near the engine. The other thing to consider is that more air usually comes at the cost of slower air flow. This reduces the vacuum in the intake and can cause problems with the MAP.