Just got back from the Ford dealer and here is what they found:
The wire harness to the security module was not connected.
Funny thing I never went under the dash.
We have owned this Expy for 3.5 years and it has never been connected.
I can say that because now we have a "Theft" light on the dash panel right below the 3 on the tac that lights up red when the security system is tripped.
Who knows why the truck was working for so long. Maybe something to do with the battery being disconnected.
It cost me $118 for the labor and no parts needed.