We describe the development of a MADX-to-Xsuite simulation framework for the Fermilab Main Injector (MI) along with the subsequent evaluation of transition-crossing behaviors in the accelerator. In particular, we studied the introduction of quadrupole magnets into the lattice as part of a transition-jump system that will be implemented in the machine through the Second Proton Improvement Plan (PIP-II). Simulated beam losses spurred by transition-induced instabilities were assessed under several systematic effects, including MI quad errors, magnet-to-magnet variability in the jump magnets, emulated power supply errors, and timing jitter.