If you install the PCM relocation bracket the hole that you will be using will effectively be cut in half. The wireharness coming off the PCM is too short to move it completely out of the way, and I think they designed it so it (the PCM) gets some cooler air moving around it (by including in the stock air box, or leaving it located near one of those holes where the stock box would draw in outside colder air.) Additionally the amount of energy you gain by installing the filter out of the engine compartment may be eaten up by a. the bends (turbulence) in the intake pipe, and b. the fact that the cooler air still has to pass through the engine compartment. If you were to do it (I would'nt) buy a IAT relocation harness and relocate your IAT sensor outside of the engine compartment, or just install the resistor mod (with leaving the IAT sensor on).
I installed a Thrasher CAI box, some members have seen the pics, Silverbullet and I actually had some pretty lengthy conversations about it on bonnevilleattitude when it was still around. Here are some pics if you want to see what it looks like..you can get a better idea for how much space you are going to have to work with when you pull out that stock air box..
(SLOW LOAD FOR 56K and less)