A method of operating a printer enables printheads mounted on print bars to be operated to compensate for misalignment of printheads in the process direction. The method includes identifying a position in the process direction for each printhead in a plurality of printheads, selecting one of the identified printhead positions as a reference printhead position, identifying a printhead timing parameter for each printhead mounted to at least one print bar, generating a firing signal for the printheads mounted to the at least one print bar, and adjusting delivery of the firing signal by the identified printhead timing parameter for each corresponding printhead mounted to the at least one print bar to coordinate actuation of inkjet ejectors in the printheads mounted to the at least one print bar and compensate for misalignment of the printheads in the process direction.