Computational simulations of the flow within a streamline-traced, external-compression supersonic inlet for Mach 1.664 without and with vortex generators were performed to refine the characterization of the inlet performance as measured by the total pressure recovery and the radial and circumferential total pressure distortion indices at the engine face. The refinement of the simulations concerned two aspects: 1) refinement of the grid for the simulations to evaluate and reduce uncertainty, and 2) refinement of the modeling and design of the vortex generators. The vortex generators studied were rectangular vane-type vortex generators arranged in co-rotating arrays within the subsonic diffuser. The vortex generator geometric factors of interest included the height, circumferential spacing, and angle-of-incidence. The flow through the inlet was simulated numerically through the solution of the steady-state, Reynolds-averaged Navier-Stokes equations on multi-block, structured grids using the Wind-US flow solver. The vortex generators were simulated using either a vortex generator model or with grids generated about each vortex generator. Statistical methods were used to compute confidence intervals and grid convergence indices to establish the uncertainties of the analyses with respect to grid refinement. Design-of-experiments methods were applied to quantify the effects of the geometric factors of the vortex generators. The analyses of the computed results illustrate the complexities of quantifying the uncertainties of the inlet performance and the implications of the uncertainties for the design of a vortex generator array for the STEX inlet.