After adding fuel and starting back up it runs rough for like 5 minutes

This is a common issue. Most likely a EVAP purge valve. It would need to be properly diagnosed to tell for sure, but we see this a lot. Give us a call if we can help you to resolve this issue. Thanks Nick

In addition, to help prevent this problem - 'never' top off tank when refueling .. When the gas pump nozzle clicks off first time, that's full enough!