Boundary layer stability analysis is performed by CFD simulation of experiments conducted in the NASA Langley Research Center 20-Inch Mach 6 air tunnel in support of the first flight of the Hypersonic International Flight Research Experimentation (HIFiRE) program. From the laminar CFD flow solutions, disturbances are calculated using the linear PSE method to obtain integrated disturbance growth rates (N factors). Comparisons are made between the experimentally-measured transition locations and the results of the PSE analysis. Roughness calculations are also performed and Reynolds number based on trip height (Rek,) is correlated with experimental results. This is a companion paper to the experimental results presented in the paper "Aerothermodynamic Testing of the HIFiRE Flight 1 Vehicle in the LaRC 20-Inch Mach 6 Air Tunnel."