An interactive divertor and scrape-off layer plasma/two-dimensional neutrals/core plasma particle and power balance model has been used to investigate the importance of uncertainties or inadequacies in the data and modeling of atomic/molecular phenomena in the divertor to the calculation of the core and divertor plasma physics parameters in a tokamak. Treating recycling as being in the form of molecules rather than atoms as well as the inclusion of reabsorption of Lyman alpha radiation in the divertor are found to have large effects on the calculated plasma and neutral parameters throughout the divertor, scrape-off layer, and core. Whether the global parameters are changed if a significant fraction of the molecules are vibrationally excited has been tested; while molecular excitation does change parameters in the recycling region in front of the divertor plate, the effect on other divertor, scape-off layer, and core plasma parameters is negligible. Estimated uncertainties in the rates for charge-exchange and elastic scattering also have a very small effect on the global parameters. Inclusion of neutral-neutral scattering, while important for the calculation of local properties in the recycling region, has only a small effect on the global parameters.