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Checking the MAF frequency and changing the curve to suit should work. I have actually done this once before to improve emissions in an early experimental HSV engine (new air intake completely changed the airflow characteristics). Normally it would be done on a proper test bench with the entire air intake setup - but that isn't going to be easy to do in your case.
A real quick and dirty way to do it is to see how much your fuelling is compensating (for example, -12%), and just pull out 8% or so from the predicted airflow in your MAF curve . If the fuelling heads the right way, then chances are you are on the right track. From there you can fine tune each frequency point as required.
The MAF curve is obtained by testing the entire intake system with the MAF in it, not just the MAF itself. That alone indicates that the intake plays a part in the MAFs response to airflow changes. Otherwise we would just get a curve from the MAF manufacturer and use that.
I'd imagine that the difference is due to changes in airflow/reversion etc around the MAF depending on the geometry of the intake.
As an example: We had a car a while ago that all of a sudden would hardly idle. After some investigation, it was found that a thermocouple had been placed in the intake, about 4 inches in front of the MAF. That was enough to make the airflow so turbulent in the MAF that it was getting airflow swings as high as 50% at steady state.