If K&N makes a FIPK kit for your application, they probably know what they are doing. When K&N makes their products, they have to make sure they are legal in all 50 states.
The people at FORD are trained to say anything aftermarket is not a good idea because it could void your warrantee. This is true in some cases. If you install an after market lift and your wheel bearings wear out to soon, then yes, it was probably due to the lift. If your stereo stops working, this is not due to the lift. The same thing goes for an after market intake and exhaust. If your engine has problems after you install the modifications, it could be due to the modifications you made and FORD would not be responsible for fixing it. You would be.
If replacing the stock intake and exhaust were a bad idea, why would people like K&N, Bullydog, and others make performance upgrades for them?
Just my $0.02 worth.
White 1998 4 door KIA Sportage 4x4 w/Eibach 2.5 spring lift and TJ rear coils, 4crawler 1.5 body lift, Monroe Sensa.trac shocks, Bosch 4+ plugs, Eaton LSD, 31x10.5x15 BFG KM tires, 2.5 cat back exhaust w/SpinTech muffler