A recently derived mathematical model to compute the effective friction and diffusion coefficients of hydronium ions in hydrated polymer electrolyte membranes is described and tested for dependence on membrane-specific parameters. Contributions to the friction coefficient due to water-polymer, water-hydronium, and hydronium-polymer interactions are determined through computation of force-force correlation functions. The conventional Stokes law friction coefficient of the hydronium ion in bulk water is then "corrected" with these statistically derived contributions and the corresponding diffusion coefficient calculated. For a Nafion(R) membrane pore with an hydration level of six water molecules per sulfonic acid functional, the model was used to compute friction coefficients for various distributions of the fixed sites, and for different side chain lengths. The model showed substantial sensitivity to these parameters and predicted that for pores of fixed volume and a constant total number of sulfonate groups, the friction on the hydrated proton is the greatest for distributions with high local anionic charge density. In a second series of computations where the radius and length of the pore were varied, the model demonstrated that the proton diffusion increases with increasing channel diameter. These calculations, therefore, demonstrate the important predictive capability of this molecular-based, nonequilibrium statistical mechanical model.