07.5 MAF/Service Air Filter Help

I did a 2nd gen swap & went at the tuning myself on a 2007.5 3500. This is the 1st truck Ive ever tuned myself so yes im green..
The issue is when im gettin on the hot pedal whether it be rolling into it or straight to the floor I will sometimes get a Service Air Filter message in the overhead display...

Im assuming this is directly related to the MAF sensor scaling being off due to intake diameter changing correct?? Ive looked thru the tables and im a little confused on which one needs to be adjusted..

Under "Turbo Control" I see "AirFlow" but whats the difference between "fresh airflow estimation vs mass charge flow"?
Im guessing fresh airflow means MAF and mass charge means MAP?



Thanks in Advance