Well I had a similar problem with my 03 lightning that really puzzled me for the longest time and even Ford didn't know what it was. It was like a humming or almost grinding type noise that would happen say when my foot is on the gas just holding speed or sitting at a stop light. I finally thought about changing the IAC and that solved the issue. The IAC was going out and becomes really loud. Swapped that out and haven't had the issue since. Not saying that's what your issue could be. I would definitely find your IAC and listen to it when the noise happens.