Aside from full-throttle operation at the dragstrip, there is very little to be gained with an aftermarket intake system on a gasoline engine. Under normal operation, like 25% throttle or so, your throttle restricts the airflow FAR more than the intake system..... to the point that any reduction in intake restriction would be trivial or less.
Some do filter air better than others I am sure, I guess a K&N filkter in the stock box will do.
There has been a debate as long as I can remember, but a replacement K&N filter will not "filter" any better than a OEM Motorcraft filter. The only benefit of using a K&N (and such) is that it is re-usable.
Be careful when cleaning...as the oil based filters tend to dirty the MAF sensor causing poor performance.
IMO...the dry type filters are better. Here is what I recommend...
advanced FLOW engineering http://www.afefilters.com/
OE Replacement Filter with Pro-Dry S Ford Trucks (99-04) (gas)
Part Number: 11-10004
Shipping Weight: 2 lbs