A method and system for controlling an engine includes a normal individual cylinder fuel correction determination module determining normal pulse mode individual cylinder fuel corrections in a normal pulse mode. The system also includes a split pulse enable module operating the fuel injectors in split pulse mode having a linear pulse and a ballistic pulse smaller than the linear pulse. The system also includes a split pulse individual cylinder fuel correction determination module determining split pulse mode individual cylinder fuel corrections in the split pulse mode. The system also includes a ballistic pulse adaptation module adjusting ballistic pulse calibration values in response to the normal pulse mode individual cylinder fuel corrections and the split pulse mode individual cylinder fuel corrections to form adjusted ballistic pulse calibration values.