A stepper motor (40) is used to position the pump rack (32A) via a preloaded compliant linkage (52,54,56) in a fuel injection pump (18), thereby exercising control over the end of injection event in response to various engine operating parameters. One part (52) of the compliant linkage (52,54,56) is engaged with the output shaft (46) of the stepper motor (40). The stop (96) is provided at the zero throttle position of the engaged part (52) of the linkage (52,54,56), at the exteme distal end of its positional range. A position sensor (100) is located at a predetermined reference position away from the stop (96) to provide a signal indicative of the engaged part (52) being at that position. When the stepper motor (40) is advanced to move the engaged part (52) away from the stop (96), the pulse count to the stepper motor is rereferenced when the reference position is reached.