I just installed an Airaid intake on my '07 with the 5.4. It works great about 80-90% of the time, however once in a while (usually when I'm at speed and I'm going from not on the gas at all to getting on it), theres a hesitation and it seems to lag for a second, and I hear a low-pitched vibration and then it kicks right in. Any ideas? I followed the instructions exactly and I'm pretty confident it's sitting correctly on the throttle body.

 

The air intake allows more air into the engine and the computer may need to be flashed to increase fuel flow to the engine. That might be your hesitation problem. I can't address the other issues.