Not really posting a question here, rather a trial and error...
I have a 2006 Ford Freestar with a 3.9L V-6.. I have had an irregular popping/thumping noise in the intake area for quite some time. This is extremely common or so I've noticed by a simple google search.
I found a TSB on this particular issue. It would seem Ford knows about the problem and says it is simply a programming error causing the Idle Air Control Valve to open and close at the incorrect time. They say a simple reprogram of the PCM with the updated software would fix the issue.
Now wait a minute, my van didn't do that new.... What does the program have to do with it, it never changed? But, I went along like a good little sheep and paid to reprogram the PCM. Guess what, it didn't make a difference. So I decided to investigate and upon unplugging the IAC (Idle Air Control) valve, low and behold the noise went away. Which brings me to my current prognoses, it must be dirty or sticky.....
I have read several blogs instructing a simple cleaning, and then several saying that is ridiculous and a mere temporary fix. So I have decided to replace it. Now in my experience with this van if it isn't Motorcraft brand, it won't last or work right. So save your self the time and frustration and order what was designed for your car, not aftermarket.
Aftermarket Brand $ 47.99
Motorcraft Brand $ 56.99
Motorcraft Brand from a reputable dealer online $ 41.00 (bought it, what a deal)
Those of you who are looking for the correct IAC valve for your Freestar or Monterey years 2004-2007 it is Motorcraft Part # CX-1771. This part fits all engines available in these model years.
Search eBay, Amazon, and Google. Got mine from eBay. I have yet to install it as it is not yet here. But, when I do I will post back the results, and hopefully it will be to say the noise is gone.