High-performance computations on Blue Gene/P at Argonne's Leadership Computing Facility have been used to determine phase shifts induced in injected RF diagnostics as a function of electron cloud density in the Main Injector. Inversion of the relationship between electron cloud parameters and induced phase shifts allows us to predict electron cloud density and evolution over many bunch periods. Long time-scale simulations using Blue Gene have allowed us to measure cloud evolution patterns under the influence of beam propagation with realistic physical parameterizations, such as elliptical beam pipe geometry, self-consistent electromagnetic fields, space charge, secondary electron emission, and the application of arbitrary external magnetic fields. Simultaneously, we are able to simulate the use of injected microwave diagnostic signals to measure electron cloud density, and the effectiveness of various mitigation techniques such as surface coating and the application of confining magnetic fields. These simulations provide a baseline for both RF electron cloud diagnostic design and accelerator fabrication in order to measure electron clouds and mitigate the adverse effects of such clouds on beam propagation.