The MultiScale ThermoHydrologic Model (MSTHM) is used to predict thermal-hydrologic conditions in emplacement drifts and the adjoining host rock throughout a proposed nuclear waste repository. This modeling effort simulates a lower-temperature operation mode with a different panel loading than the repository currently being considered for the Yucca Mountain license application. Simulations address the influence of repository-scale thermal-conductivity heterogeneity and the influence of preclosure operational factors on thermal-loading conditions. MSTHM can accommodate a complex repository layout, a development that, along with other improvements, enables more rigorous analyses of preclosure operational factors. Differences in MSTHM output occurring with these new capabilities are noted for a new sequential waste-package-loading technique compared with a standard simultaneous-loading technique. Alternative approaches to modeling repository-scale thermal-conductivity heterogeneity in the host-rock units are investigated, and a study incorporating geostatistically varied host-rock thermal conductivity is discussed.