Phil is right, doing a quality air intake kit will not cause a need for more custom tuning in that vehicle, you still have a traditional MAF meter.
While I don't really care for K&N's FIPK kits for these vehicles, they generally do add some power - about 8-10 HP on a 4.6 and about 10-13 or so HP on a 5.4 in the F-150 & Expedition - and there's no getting around the traditional "intake moan" that will happen any time you reduce restriction in the air intake tract. But the intakes we use are quiet during periods of low loads, they only get louder when the engine is under a heavier load - for example, when you romp down on the gas pedal, it sounds kinda like an old 4-bbl. carb when you opened up the secondaries.
I don't know what problem you had with your FIPK kit - there have been some F-150 owners who complained about the mounting setup for the FIPK, with it chafing one of the wiring harnesses depending on which assembly line that truck was built on, there was some difference in the routing of one of the harnesses, and that would sometimes cause interference with the FIPK - but they always gained some power. What has to be remembered about air flow mods in the 1997-2003 F-150's (and most other vehicles) is that they work best when the engine is breathing harder - when the engine actually needs more air. An intake kit or a cat-back exhaust will add power, but they aren't going to (alone) give anyone some big seat-of-the-pants gain in a 5000 lb truck or SUV - but those mods are indeed well worth doing *if* you select the correct brand of part - that's what we do, is test them, to determine which is doing the best job, so when you get our Stage kits or add them on one piece at a time, you'll always be getting the very best available, and get the best possible result. We try to give approximate power gains & performance differences in our listings for our various Stage 1 thru Stage 5 Troyer Performance packages you'll see on our web site.
Overall, the actual order of bang for the buck is to do the tuning first, then the intake kit second, and then the cat-back exhaust 3rd. Then from there, you can do the rest of the Stage 2 components for the 1997-2003 F-150 and 1997-2004 Expedition in just about any order you like. Now if you are going to eventually go on to do the Stage 2 over time (and for your 2004 Expedition, we would want to do a custom Xcalibrator-based version of our part# "Stage2-COP," so you've started our correctly with the custom-tuned Xcalibrator), then we should know that up front so we can bump up the idle speed a little bit in your custom tunes for the E-fans & underdrive pulleys - that is something we like to do for those with E-fans & underdrive pulleys, just so you have full normal current from the alternator - like when driving in summertime at night, when you come to a stoplight - you will have everything on, the headlights, the A/C, maybe both of the fans, etc. - we bump the idle speed up just slightly to insure full available normal alternator output at idle. Anyway, just let us know that and we will do that up front in your custom tuning, and that way nothing else needs to be changed all the way thru our Stage 2 level - you can just let one of our staff know and they'll make a note on your custom Xcalibrator order, if they haven't already.
So that's the deal - we recommend doing the custom tuning first, then the intake, then the exhaust, and then you can do the E-fans, underdrives & ignition upgrade to complete Stage 2 in any order you want. You can actually do anything in our Stage 2 for the V8's in any order you want, we generally advise doing the first 3 in their basic order of "bang for the buck" - which is tuning, then intake, and then the exhaust.