The density of states diagrams, and the associated orbital populations and structure, are analyzed for the discrete models for dithiol bridged molecular junctions discussed in the previous paper. The orbitals closest to the Fermi surface are generally dominated by the high s and d densities of metal atoms. Some orbitals are mixed metal/sulfur/hydrocarbon, and a few (generally lower-lying occupied) are dominantly within the hydrocarbon itself. These orbital populations suggest that the frontier orbitals are, in themselves, not adequate for quantitative description of transport, essentially because the Green's functions of slightly lower-lying orbitals give large contributions to the mixing between electrodes that dominates the transport. Effects of different spin multiplicities and charges, as well as different choices of density functional, are also presented: the major conclusions seem robust, and are not strongly effected by these modifications. (C) 2003 American Institute of Physics.