Herbig-Haro objects are the nebulous emission regions arising from shocks associated with the bipolar outflows of young stellar objects. Observations of the emission lines of HH objects can reveal properties of these stellar jets, which are associated with star formation, and one tool to study stellar jets and HH objects is computer modeling. AstroBEAR is a 3D magnetohydrodynamic code with adaptive mesh refinement and parallelization capabilities. The goals of this research were (1) to improve the cooling in AstroBEAR and add the ability to create valid emission-line maps for HH objects, and (2) to model a jet overrunning and shocking clumps, and to explore a parameter space that may lead to morphologies like those of HH 29. The results generate emission-line maps with the correct spatial morphology in Hα and [SII], and begin to map out the regimes (shock velocities, resolution, physical scales) in which the code remains valid.