I changed the mass air flow sensor . Car is OK during the day but have to unplug in morning or night . Does the pcu or something need to be reprogrammed ?

No, just make sure all old codes are cleared from the PCM.

Can I clear the pcm without going to the dealer ?

Yes, use any code reader or scan tool to clear all codes. Many auto parts stores make them available for free.

One more question ; can these codes be actually affecting the way it runs ? My main symptom is it runs good all day but I have to unplug the sensor at night or the car won't turn over .
Thanks for your time