This paper presents a novel grid generation scheme for the numerical simulation of hypersonic nozzle flows. The grid is based on the characteristic lines of the supersonic regions of the flow. This allows for grid alignment and clustering along disturbances such as expansion and compression waves present in the flow. This gridding method allows for high resolution computational fluid dynamics (CFD) simulations of the flow in the Arnold Engineering Development Center (AEDC) Hypervelocity Tunnel 9 Mach 14 Nozzle. Simulations of the nozzle are performed in order to quantify how wall contour imperfections in the nozzle affect the core flow of the nozzle, particularly in the test section. Previous studies of the nozzle resulted in disagreement between CFD prediction and experimental measurements. Although these disagreements have not been fully resolved, a loss mechanism has been identified in the form of waves generated by the wall imperfections, and significant improvement has been made in the quantitative understanding of the flow in the nozzle.