I think the stock intake box is fine. Just take out the silencer and install a flat k&n.
I took this farther and drilled a 3" hole in the sheet metal in front of the airbox and put a 3" tube in it, and connected it using tube connectors I found in the "ricer" section of autozone. Then I insulated the intake box.
I used to run an open element K&N (rustys off road kit) thinking it improved performance, but it actually hurt it because it was sucking hot engine air. My throttle response was lazy. So I took it off and built the system described above, and the sharp throttle response returned.
Some might say "Why don't you insulate the open element?", well for 2 reasons, it doesn't look as clean, and at high rpms there is so much suction that the insulation would stick to the filter causing a flow restriction. I could build some kind of a frame to hold the insulation but I figured the extra performance from a cone filter as opposed to a flat filter wouldn't be that much, so I put the stock air box back on.
Another area I found extra low end torque in is the thermotec intake manifold heat shield Dr. Dyno did. He said he got 4 lb-ft at 1000 rpm, which sounds reasonable for the older intake manifolds, but since I have the bigger 99+ intake (more metal = more heat capacity) I'd put that figure around 5 or 6 lb-ft. These gains aren't that noticeable in any type of driving on pavement, but they are DEFINITELY noticeably when going slow off road, because airflow is slow and the intake manifold normally gets so hot you could cook off it.
