Our understanding of physical processes in photodissociation regions or photon-dominated regions (PDRs) largely depends on the ability of spectral synthesis codes to reproduce the observed infrared emission-line spectrum. In this paper, we explore the sensitivity of a single PDR model to microphysical details. Our calculations use the Cloudy spectral synthesis code, recently modified to include a wealth of PDR physical processes. We show how the chemical/thermal structure of a PDR, along with the calculated spectrum, changes when the treatment of physical processes such as grain physics and atomic/molecular rates are varied. We find a significant variation in the intensities of PDR emission lines, depending on different treatments of the grain physics. We also show how different combinations of the cosmic-ray ionization rate, inclusion of grain-atom/ion charge transfer, and the grain size distribution can lead to very similar results for the chemical structure. In addition, our results show the utility of Cloudy for the spectral modeling of molecular environments.