The problem here is:
The LT1 MAF signal is not what you want to measure.
How do you know that the min-AFC output is accurate?
This is the signal that goes out to the PCM.
For instance when the MAF is generating a 1000 Hz signal the AFC should be adjusting that to 820 Hz.
This is where an oscilloscope would be helpful. You could measure the actual frequency and compare it to the reading on the Aeroforce.
I guess you could play around with MAF calibration in HPT but this is like throwing darts in the dark if the signal from the AFC is non-linear...which I would guess is the case.
The tuning guys on here would probably like to know more about your setup. I'm sure they can help more than I.