Glad to here the good news and that you like it!
The idle should pick up after awhile. What has happened is the pcm has gotten new calibrations and limits it has to relearn and sometimes a lower idle is a result of this. Another thing is to inspect the throttle body if its dirty and gunky that could be the other reason.
The extra plug on the cord isn't for the gas F150 application, so don't worry about it.
Peace!