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Originally Posted by landrovered
The only part of the post combustion cycle of the engine that enters into the ECU EFI functions are the o2 sensors. The ECU does not care how quickly the exhaust gasses leave the cylinder, only the completeness of the combustion and the effectiveness of the cat. The MAF would reflect and correct for the greater flow through of the engine and the pulse width of the injectors would be set according to the fuel curves.
In short, headers not being taken into account would not cause the sort of problems the OP is describing.
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You have provided an excellent answer to the question. However, if the MAF is not properly correcting air flow and fuel mixture due to a change in headers and cats, even if this is occurring on a low detection level, is it possible that re-mapping the ECU to increase these mixtures can exacerbate the problem ?