We present experimental work with a new atomic force microscope-based technique that attempts to elucidate the electronic structure of aromatic metal-molecule-metal junctions. In addition, we have also used this technique to perform preliminary studies on the relationship between the thermoelectric properties of molecular junctions and their molecular structure, the coupling strength of molecules to the electrodes, and the end groups of the molecule. The low-bias electrical conductance of junctions was found to be exponentially dependent on length and strongly affected by the coupling strength of the molecules to the electrodes. The low-bias electrical conductance of junctions was found to be exponentially dependent on length and strongly affected by the coupling strength of the molecules to the electrodes. The current-voltage characteristics of junctions of various molecular lengths were also analyzed using transition voltage spectroscopy. The transition voltage was found to decrease with increasing molecular length, indicating that the energetic separation between the chemical potential and the closest molecular orbital decreases with increasing length. Secondly, based on an analysis of our thermopower measurements using the Landauer model, electronic transport through aromatic thiols of various chain lengths was deduced to be HOMO dominated. The Seebeck coefficients for a series of dithiol molecules were also measured and were almost identical to corresponding values of the monothiol series. This suggests that coupling strength does not play a role in the magnitude of a junction’s thermopower, or equivalently, that the relative electronic alignment of molecular orbitals with respect to the Fermi level of the electrodes is unchanged by coupling strength. However, contact chemistry can play a significant role in molecular level alignment, as evidenced by the change in sign of the thermopower of a junction formed from an isocyanide-terminated monolayer. This sign change suggests a shift from HOMO- to LUMO-mediated transport in isocyanide molecules.