The stock MC is like most Ford units, over optimistic for MPG, and the rest too. I've found them to be about 10% off in the several Fords I have had, 80's and 90's. Altering the actual fuel use will likely make it more noticeable, the system isn't really able to sense any extra fuel consumption versus stock. Your tuner is probably on the right path if it can be adjusted, the PCM fuel use PIN might be possible to manipulate. I have always wanted to look into that, I had to deal with it first in 1998 when I swapped a Mustang MAF PCM into my 91 Mark VII(speed density). I lost the cruise control(inside the Lincoln PCM), but the fuel data stayed fairly normal.