Transport in metal-molecule-metal junctions is defined by the alignment and coupling of molecular orbitals with continuum electronic states in the metal contacts. Length-dependent changes in molecular orbital alignment and coupling with contact states were probed via measurements and comparisons of thermopower (S) of a series of phenylenes and alkanes with varying binding groups. S increases linearly with length for phenylenediames and phenylenedithiols while it decreases linearly in alkanedithiols. Comparison of these data suggests that the molecular backbone determines the length dependence of S, while the binding group determines the zero length or contact S. Transport in phenylenes was dominated by the highest occupied molecular orbital (HOMO), which aligns closer to the Fermi energy of the contacts as approximately L(-1), but becomes more decoupled from them as approximately e(-L). In contrast, the decreasing trend in S for alkanedithiols suggests that transmission is largely affected by gold-sulfur metal induced gap states residing between the HOMO and lowest unoccupied molecular orbital.