We present Keck Interferometer observations of T Tauri and Herbig Ae/Be stars with a spatial resolution of a few milliarcseconds and a spectral resolution of ∼ 2000. Our observations span the K-band, and include the Brγ transition of Hydrogen and the v = 2 → 0 and v = 3 → 1 transitions of carbon monoxide. For several targets we also present data from Keck/NIRSPEC that provide higher spectral resolution, but a seeing-limited spatial resolution, of the same spectral features. We analyze the Brγ emission in the context of both disk and infall/outflow models, and conclude that the Brγ emission traces gas at very small stellocentric radii, consistent with the magnetospheric scale. However some Brγ-emitting gas also seems to be located at radii of 0.1 AU, perhaps tracing the inner regions of magnetically launched outflows. CO emission is detected from several objects, and we generate disk models that reproduce both the KI and NIRSPEC data well. We infer the CO spatial distribution to be coincident with the distribution of continuum emission in most cases. Furthermore the Brγ emission in these objects is roughly coincident with both the CO and continuum emission. We present potential explanations for the spatial coincidence of continuum, Brγ, and CO overtone emission, and explore the implications for the low occurrence rate of CO overtone emission in young stars. Finally, we provide additional discussion of V1685 Cyg, which is unusual among our sample in showing large differences in emitting region size and spatial position as a function of wavelength.