When installing a new MAF they say it is recommended to reset the ECU to basic factory settings by disconnecting the car battery for 5-10 minutes (the ECU settings will have been messed up by the bad MAF).

Then start the car and let it run for about 5-10 minutes at idle to allow the ECU recalibrate to the new MAF. Then take the car for a drive and excercise the engine over the complete RPM range. The complete calibration will be done over a few runs.

Yes, the engine will run rough with a perfectly good brand new MAF when you first start it if you don't reset the ECU...