A machine is disclosed. The machine may have an engine having a combustion chamber. The machine may also have a first sensor configured to generate a first signal indicative of a speed of the combustion engine. Additionally, the machine may have a second sensor configured to generate a second signal indicative of a desired supplied fuel quantity. The machine may also have a counter configured to generate a third signal indicative of a count. Additionally, the machine may have a fuel injection system having a controller. The controller may be configured to, based on the first, second, and third signals, select one of a plurality of shot modes and generate a corresponding fourth signal. The fuel injection system may also have a fuel injector configured to, based on the fourth signal, inject a quantity of fuel into the combustion chamber.