2010 Forester - Misfire after engine replacement

[orwigd]

Just got a new warranty engine installed in my 2010 forester (EJ25 non turbo) by a shop. Got it back and after 5 miles of drive time it threw codes for all 4 cylinders saying they had a misfire. Further pressed the wires onto the spark plugs and got rid of the cylinders 3 & 4 misfires. Then replaced spark plug wires, spark plugs, and ignition coil and got rid of the cylinder 1 misfire. Then installed a new injector for cylinder 2 and got rid of that misfire for about 24 hours. Drove it again and after about 25 miles of drive time cylinders 1 and 2 misfire came back again. Has anyone had this problem before and what did you do to fix it? Cannot figure out what it is. The shop told me pointless solutions that didn't fix the problem. Mass Air Flow Sensor has also been replaced.