when they talk about the 5.4 with or without the egr, what are they talking about? thanks

 

EGR = e xhaust g as r ecirculation system.
It is a vacuum gating device that senses exhaust pressure and opens a valve to let exhaust gas into the intake stream.
The purpose is to reduce combustion chamber temperatures that qreatly reduce nitrogen oxide emmisions during the time the engine spends most of it's time running at.
This operation takes place mainly at cruise and light load condtions, never at idle or wide open throttle.
You can see from this that, for instance, an EGR valve stuck open would cause a very rough idle as well as setting a code.
When it is called into operation, there are other things that happen within the computer program that make it's operation transparent to you, as you drive.