Given a supernova with stellar mass $M$, is there a theoretical method to estimating the isotope yield? If so, what processes are taken into account, and how accurate can the estimate be? Would it be more accurate if more properties were known about the star (e.g. metallicity)?
You have to run a massively sophisticated supernova simulation to get that kind of data. Whole research groups work on them. The biggest unknowns are generally the details of neutrino physics. This is both because neutrino hard data doesn't come easy, and because solving the radiation field of a supernova is a function of seven or eight variables (x, y, z positions, two angles for direction of radiation propagation, energy band, polarization, and time). Trying to obtain decent resolution in all of those variables quickly becomes computationally explosive. Try Google Scholaring "Supernova Yield".