It could be a couple of things... First thing is have your computer read by a scanner. Auto Zone will read codes for FREE. And go from there. I had a similar problem on my 1998 Ford Expedition XLT, and it ended been bad spark plugs. And since I have the 4.6L on mines I had to change plugs and wires. Problem was fix. The 4.6L only has 2 coil packs too... But, since you have the 5.4L it could also be bad coil packs... There 8 coil packs on the 5.4L.
I'm not a mechanic / technician but I was looking at a picture on fordparts.com and it shows the mass airflow sensor located around the engine air filter assembly on the drivers side for a 2006 Ford Expedition
It does not have a mass airflow sensor.It does not have a mass airflow sensor.
It does not have a mass airflow sensor.It does not have a mass airflow sensor.
It does not use a mass airflow sensor.It does not use a mass airflow sensor.
It does not have a mass airflow sensor.
It does not have a mass airflow sensor.
It does not have a mass airflow sensor.It does not have a mass airflow sensor.
It does not have a mass airflow sensor.It does not have a mass airflow sensor.
A Dodge Neon does not have a mass airflow sensor.
On a 1999 Ford Expedition : The Mass Air Flow sensor is between the engine air filter and the large diameter engine air intake tube ( it is INSIDE a round shaped plastic housing )
A Chrysler LHS does not have a mass airflow sensor.
It doesn't have a mass airflow sensor.It doesn't have a mass airflow sensor.