Bought a 2010 Eddie Bauer with the 5.4L to use a tow vehicle. After a trip through the Shenandoah Valley & surrounding "mountains" towing our pretty hefty travel trailer (6000 lbs) I noticed a bit of a tap. Vehicle had 95k miles on it and looked like it still had stock plugs and coil packs etc so I figured I'd do a quick tune up.
New plugs, new coil packs, aftermarket MAF, K&N CAI and Edge programmer.
Set the programmer for tune level 2, which is their "towing" tune and noticed a decent improvement in torque and a minimal improvement in MPG but then also noticed a weird rattling/tapping that sounded like something between an exhaust leak and a valve tapping but only really noticed it under load (eg. in idle, didn't notice it but put it in drive you could hear it, give it gas and you can hear it more) and to varying degrees. Sometimes worse than others and seemed to be coming from behind the passenger foot well / firewall.
Removed the CAI and MAF and programmed back to stock but still had the noise, but noticed it seemed to change in intensity and thought it might have been the relearn process taking a long time to settle down, but it never did go away and seemed to recently get worse but isn't throwing any codes via the Edge ODB III reader.
Took it in yesterday and they are saying it's the catalytic converter so I'm guessing I just pushed it too hard through the mountains (there were a few times we were pushing 5500+ RPMS getting up and around the mountains) and my less than exciting results from the CAI/MAF etc were more to do with the cat going bad than any sort of issue with the products and the Ford computer.
Now I'm on the lookout for a new reasonably priced exhaust system, including a cat, and once that's done I'll try throwing the CAI and MAF back on and re-tuning it.