Polarity of the wires on the crank trigger sensor will likely affect your timing on a MSD Ignition System. MSD advises that the correct polarity is the one that has the most timing advance on a Digital Ignition. For analog ignitions, this is opposite, and the correct polarity is the one that has the most retard. You must try both polarities to see which one generates the most advanced setting on a digital ignition (or most retard on analog ignition).
SBF Crank Trigger Installation Instructions [PDF Format].