A system according to the present disclosure includes a spectral density module and a firing sequence module. The spectral density module determines a spectral density of engine speed. The firing sequence module selects a first set of M cylinders of an engine to activate, selects a second set of N cylinders of the engine to deactivate, and selects a firing sequence to activate the first set of M cylinders and to deactivate the second set of N cylinders. M and N are integers greater than or equal to one. The firing sequence specifies whether each cylinder of the engine is active or deactivated. Based on the spectral density, the firing sequence module adjusts the firing sequence to adjust M and N and/or to adjust which cylinders of the engine are included in the first set and which cylinders of the engine are included in the second set.