Low pressure (<50 mTTorr) electron cyclotron resonance plasma sources are being developed for downstream etching and deposition and for production of radicals for surface treatment. The spatial coupling of microwave radiation to the plasma is a concern due to issues related to the uniformity of dissociation, electron heating, and ultimately process uniformity. To investigate these issues, a finite-difference-time-domain simulation for microwave injection and propagation has been developed, and has been incorporated as a module in the two-dimensional Hybrid Plasma Equipment Model. Results from parametric studies of N-2 plasmas suggest that obtaining uniform fluxes to the substrate may require a power deposition profile that is peaked off axis. An increase in power deposition tends to reinforce nonuniformities in the ion flux profile. At higher pressures (>10 mTorr) the sensitivity of the ion flux to the substrate to the angle of the magnetic field at the substrate decreases, while the uniformity of the ion flux improves. Due to the dependence of the collision frequency on electron temperature, losses from cross-held diffusion are enhanced in both the low and high pressure regimes. Results also suggest that there is an optimal pressure for maximizing both the magnitude of the ion flux to the substrate-surface and its uniformity.