If the MAF sensor housing inner diameter changes in any way, the calculation performed by the engine management system will be incorrect. This means that the amount of air actually entering the system will be different from what the computer thinks is entering the system. This is critical because the computer determines how much fuel and timing to run based on this value of air. When it's wrong, it can cause the engine to run richer, or leaner, than it should.
With aftermarket intakes, it's extraordinarily common for the piping used to have a different inner diameter than the MAF sensor housing incorporated in the factory air box. This is due to the fact that the exact inner diameter of the factory MAF sensor housing is different than what's commonly available in the standard metal piping used for aftermarket intake systems.
It is true that some aftermarket intakes show an increase in power when installed on a stock vehicle. This power increase is due to the fact that the aftermarket intakes have a larger inner diameter for the MAF sensor housing to mount into which in turn leans out the Air/Fuel mixture because of this error in calculating how much air is actually entering the system.
Please note this is NOT due to the fact that the aftermarket intake is so much less restrictive than the stock air box and therefore more air is getting in but rather that the computer does not know it's now sucking from a larger tube and therefore more air is getting in.
So to recap, whenever the MAF sensor housing size is increased compared to stock, more air will enter the system than the engine management has been calibrated for and you will run leaner. If the MAF sensor housing size is decreased compared to stock, less air will enter and you will run richer.
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