If you are testing aero mods, the important data is how much fuel you use to maintain speed. Aero doesn't make acceleration more or less efficient. What you are interested in, IMHO, is the FE once you get up to cruising speed.
So, accelerate to a speed where aero will make a difference (preferably with cruise control), reset your trip average, drive for some distance, and observe your numbers. When you switch from A-B and back to A, be sure to have the same speed and use the same lane, start point, and stop point.
That way your acceleration won't skew the data too much (hopefully at all).
Am I mistaken somewhere?
EDIT: I just realized I dug up a sorta old one
