2007 honda pilot misfiring on 4 cylinders


I have a 2007 honda pilot 4wd with 156,000 miles. After driving for about a half hour I stopped and parked. I restarted the car about 15 minutes later and the car was running rough and the check engine light came on. I took the car to autozone and they scanned the computer and the codes for misfiring came up for 4 out of 6 cylinders. My mechanic has since replaced all of the 6 ignition coils with OEM coils. The spark plugs were replaced at 120,000 miles with OEM plugs. I verfied that all the parts he has ever put in were OEM before he installed them. He showed me the boxes and gave me the old parts in the new part boxes. The battery and alternator were both checked and are fine. The car still seems to run a little rough up on start up but the check engine light has not come back on. I have run fuel injector cleaner through a few tanks of gas (the good kind that you suggest). Any idea why so many misfire codes would come on at one time after only sitting for 15 minutes? Did the mechanic diagnose the wrong problem? Could the injectors or fuel pressure regulator be bad? The car has the original fuel pump and regulator as well as fuel injectors.