Recently we have presented theoretical predictions and numerical modeling that show that a more advanced processing scheme can significantly improve the performance of photoelastic modulator (PEM)-based Mueller polarimeters. Of note, by simply including all of the multi-carrier harmonics rather than a hand-selected subset thereof, the sensitivity of the system can be enhanced by up to a factor of six in certain elements of the Mueller matrix. This paper extends our work on PEM-based Mueller polarimeters to PEM-based partial Mueller systems with 2 PEMs, one PEM each in the generator and analyser. Our findings clearly demonstrates significant performance improvement through the use of a substantially large set of multi-carrier harmonics rather than a hand-selected subset. We also present results from our experimental PEM testbed system that verifies the numerical findings.