Spatial heterodyne interferometry (SHI) is a technique based on Fourier transform spectroscopy. As such, many of the benefits, such as high spectral resolving power, can be realized. Furthermore, unlike a Fourier transform spectrometer, an SHI is able to minimize the number of required samples for a given resolving power and spectral range. The calibration and detailed modeling of a polarization spatial heterodyne interferometer (PSHI) are detailed. Unlike our original first-order ray tracing model, the new model is based on the Jones matrix formalism. Using this improved model, we explore the nonideal aspects of the PSHI, including interference effects caused by retardance errors in the polarization grating and quarter wave plate. To minimize the influence of these errors, a calibration procedure is described based on a linear operator theory. Finally, the Jones matrix model and calibration procedure are validated through a series of simulations and experiments.