An apparatus includes an input module structured to interpret a fuel pressure command indicative of a target fuel pressure within an accumulator and a target fuel injection characteristic, a pump module structured to control a pump assembly to provide fuel to the accumulator to maintain the target fuel pressure within the accumulator, an injector module structured to control a plurality of fuel injectors to inject fuel into an engine based on the target fuel injection characteristic, a pressure module structured to interpret pressure data regarding an actual fuel pressure within the accumulator and to determine a pressure difference between the target fuel pressure and the actual fuel pressure, and a modulation module structured to determine a final fuel injection command responsive to the pressure difference exceeding a first magnitude threshold where the final fuel injection command is based on the pressure difference and the target fuel injection characteristic.