2001 Ford F-150 post fuelpump and complete tune up

Ok. My fuel pump went so I dropped the tank and changed it. It was difficult getting started after the change but it finally started. And ran really rough for the next day or so. Added injector cleaner and seemed better but not 100%. So I did a complete tune up and again. It seemed better for a week or so. And again began running rough. Changed the fuel filter again thinking maybe dropping the tank dislodged dirt or something. Now the service engine soon light is on so I took it to autozone to have coded. Misfire cylinder 2 comes up. Take the plug out and I change it even though it seemed fine. Reinstall the coil and it still comes up misfire cylinder 2. Heres my question. If the coilis bad will the code come up bad coil or could that be the mis fire in cylinder 2. Or could a clogged injector maybe cause the misfire all of this happened after I changed the fuel pump.I'll have days where it seems like theres nothing wrong with the truck. Can a intermitten fuel pump cause a misfire. Fuel regulator. Very puzzling