Large area molecular junctions consisting of covalently bonded molecular layers between conducting carbon electrodes were compared for Co and Ru complexes as well as nitroazobenzene and anthraquinone to investigate the effect of molecular structures and orbital energies on electronic behavior. A wide range of molecular layer thickness (d) from 1.5-28 nm was examined and three distinct transport regimes in attenuation plots of current density (J) vs thickness were revealed. For d < 5 nm, the four molecular structures had comparable current densities and thickness dependence despite significant differences in orbital energies, consistent with coherent tunneling and strong electronic coupling between the molecules and contacts. For d > 12 nm, transport depends on the electric field rather than bias, with the slope of ln J vs d near-zero when plotted at a constant electric field. At low temperature (T < 150 K), transport is nearly activationless and likely occurs by sequential tunneling and/or field-induced ionization. For d = 5-10 nm, transport correlates with the energy gap between the highest occupied and lowest unoccupied molecular orbitals, and ln J is linear with the square root of the bias or electric field. Such linearity occurs for all three transport regimes and is consistent with the energy barrier lowering by the applied electric field. The results clearly indicate a strong dependence of charge transport on molecular orbital energies provided d > 5 nm, with a variation of 7 orders of magnitude of J for different molecules and d = 10 nm. The results provide insights into charge transport mechanisms as well as a basis for rational design of molecular electronic devices.