Regarding the mole fractions, 0.21 is the mole fraction of oxygen in the air and not the air itself. Rest 0.79 is occupied by nitrogen and other small amount of gases which is often ignored. The calculations you have shown will be applicable if you have the mixed reactants of methane and air at the inlet. Generally, in combustion systems there is dedicated fuel injection system and oxidizer system where you would need to input mole fraction of 1 for methane and 0.21 for oxygen respectively. And adjusting the flow rates to achieve the required air-fuel ratio.
But, as you are using mixed flow of reactants at single inlet, please use the calculated mole fractions of ch4 and o2 at the inlet. The Damkohler number for methane combustion is high (reaction is very fast and thus controlled by turbulent mixing). And as you are using only one step reaction, you should use EDM instead of FR.
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