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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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2001 Boxster S 3.6L, Zeintop
"Calling upon my years of experience, I froze at the controls." - Stirling Moss
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