Under the direction of the United States Department of Energy (DOE) National Nuclear Security Administration (NNSA) Office of Material Management and Minimization (M3) Reactor Conversion Program, the University of Missouri Research Reactor (MURR®) plans to convert from highly enriched uranium (HEU) fuel to low-enriched uranium (LEU) fuel. Low power physics startup test predictions, transition core planning, and analysis for a proposed fission-based molybdenum-99 production upgrade were done in support of LEU fuel conversion. As a first step to LEU fuel conversion, low-power physics tests will be performed to calculate reactor physics parameters. These parameters include flux distributions, coefficients of reactivity, and critical assembly measurements. To facilitate this test, reactor physics calculations were performed using MCNP5 to predict the values of these parameters. Implications of these predictions and areas of uncertainty in the prediction analysis are also discussed. Once MURR completes the testing of the initial LEU core, MURR will enter into a series of transition cycles until steady-state mixed-burnup operation is reached. A Python program was developed that incorporated the constraints of MURR operation while minimizing the time MURR will have to operate atypically during the transition cycles. The impacts of the transition cycles on experiment performance are reported, as well as the number of fuel elements needed. Finally, preliminary analysis on a proposed molybdenum-99 production device at MURR was performed. This analysis shows the impact on the reactor power distribution with implications to predicted safety margins as a part of the larger scope of the experiment analysis.