To advance the design of hypersonic vehicles, high-fidelity multi-physics CFD is used to characterize 3-D scramjet flow-fields in two novel streamline traced configurations. The two inlets, Jaws and Scoop, are analyzed and compared to a traditional rectangular inlet used as a baseline for on/off-design conditions. The flight trajectory conditions selected are Mach 6 and a dynamic pressure of 1,500 psf (71.82 kPa). Analysis of these hypersonic inlets is performed to investigate distortion effects downstream with multiple single cavity combustors acting as flame holders, and several fuel injection strategies. The best integrated scramjet inlet/combustor design is identified. The flow physics is investigated and the integrated performance impact of the two innovative scramjet inlet designs is quantified. Frozen and finite rate chemistry is simulated with 13 gaseous species and 20 reactions for an Ethylene/air finite-rate chemical model. In addition, URANS and LES modeling are compared to explore overall flow structure and to contrast individual numerical methods. The flow distortion in Jaws and Scoop is similar to some of the distortion in the traditional rectangular inlet, despite design differences. The baseline and Jaws performance attributes are stronger than Scoop, but Jaws accomplishes this while eradicating the cowl lip interaction, and lessening the total drag and spillage penalties. The innovative inlets work best on-design, whereas for off-design, the traditional inlet is best. Early pressure losses and flow distortions in the isolator aid the mixing of air and fuel, and improve the overall efficiency of the system. Although the trends observed with and without chemical reactions are similar, the former yields roughly 10% higher mixing efficiency and upstream reactions are present. These show a significant impact on downstream development. Unsteadiness in the combustor increases the mixing efficiency, varying the flame anchoring and combustion pressure effects upstream of the step.