High-resolution observations of edge-on proto-planetary disks in emission from molecular species sampling different critical densities and formation pathways offer the opportunity to trace the vertical chemical and physical structures of protoplanetary disks. Based on analysis of sub-arcsecond resolution Atacama Large Millimeter Array (ALMA) archival data for the edge-on Flying Saucer disk (2MASS J16281370-2431391), we establish the vertical and radial differentiation of the disk CN emitting regions with respect to those of $^{12}$CO and CS, and we model the disk physical conditions from which the CN emission arises. We demonstrate that the disk $^{12}$CO (2-1), CN (2-1), and CS J=5-4 emitting regions decrease in scale height above the midplane, such that 12CO, CN, and CS trace layers of increasing density and decreasing temperature. We find that at radii > 100 au from the central star, CN emission arises predominantly from intermediate layers, while in the inner region of the disk, CN appears to arise from layers closer to the midplane. We investigate disk physical conditions within the CN emitting regions, as well as the ranges of CN excitation temperature and column density, via RADEX non-LTE modeling of the three brightest CN hyperfine lines. Near the disk midplane, where we derive densities nH2 ~10$^{7}$ cm$^{-3}$ at relatively low T$_{kin}$ (~12 K), we find that CN is thermalized, while sub-thermal, non-LTE conditions appear to obtain for CN emission from higher (intermediate) disk layers. We consider whether and how the particular spatial location and excitation conditions of CN emission from the Flying Saucer can be related to CN production that is governed, radially and vertically, by the degree of irradiation of the flared disk by X-rays and UV photons from the central star.