1997 Aerostar AWD / Runs rough / check engine light stays on

Hi, We have a 1997 Aerostar AWD, 4.0, Miles 122,000. Where do I begin! Van's check engine light has been on. We have taken this van to have the codes read. After replacing the spark plugs, wires, air fliter. Codes said replace Coil, Mass Airflow Senser, and one more part I can't remember right now. (My husband does all the work on it) All that was done. Anyhow, engine seems to begin to run better, but then starts running rough and by the way the Mass airflow senser vibrates so loud, it's embarrassing! A really loud humming noise. This happens when it gets warm or sittiing in a drive thru on hot or warm days. Usually never a problem when cold. The old one did the same thing, most of the time only in the idling state. We thought replacing this would stop this problem but it has not. Back to the engine, the roughest running is at the idle. Sometimes it even shuts off. It always starts. Running low speeds and idle engine light blinks running higher speeds goes back to steady on. It was put back on the computer, they can not tell us what the problem is, all they can say is for some reason it is missfiring on the #2 and #4 cylinders. All wires have been checked and rechecked. All wires and plugs are brand new. Once in a while it seems to run better, but most of the time not. What else can we check? Help! We've put money and more money in the van with no real results yet. Thank-you!