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Q: Engine misfires and hesitates while accelerating

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Upon starting the car (always only once) it will misfire before kicking into gear. I can not accelerate before this occurs (I can rev the engine but it does not help). Also, when downshifting or after slowing down, the car will have a 5-10 second delay before full acceleration. It feels like a constant down shift is holding me back until it kicks into gear. Please note I have recently replaced my Max Airflow Sensor as the car's check engine light has been on since I got the vehicle (approx 2 years ago) due to an aftermarket air intake damaging the sensor. I also replaced the intake with a newer K&N model but it is not the standard intake made for the vehicle. The check engine light is now off, but these problems did not occur until the replacements were made.

My car has 80000 miles.
My car has a manual transmission.

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