We report here an extensive study of transport and electronic structure of molecular junctions based on alkyl thiols (CnT; n = 7, 8, 9, 10, 12) and dithiols (CnDT; n = 8, 9, 10) with various lengths contacted with different metal electrodes (Ag, Au, Pt). The dependence of the low-bias resistance (R) on contact work function indicates that transport is HOMO-assisted (p-type transport). Analysis of the current-voltage (I-V) characteristics for CnT and CnDT tunnel junctions with the analytical single-level model (SLM) provides both the HOMO-Fermi energy offset epsilon(trans)(h) and the average molecule-electrode coupling (Gamma) as a function of molecular length (n), electrode work function (Phi), and the number of chemical contacts (one or two). The SLM analysis reveals a strong Fermi level (E-F) pinning effect in all the junctions, i.e., epsilon(trans)(h) changes very little with n, Phi, and the number of chemical contacts, but Gamma depends strongly on these variables. Significantly, independent measurements of the HOMO-Fermi level offset (epsilon(UPS)(h)) by ultraviolet photoelectron spectroscopy (UPS) for CnT and CnDT SAMs agree remarkably well with the transport-estimated epsilon(trans)(h). This result provides strong evidence for hole transport mediated by localized HOMO states at the Au-thiol interface, and not by the delocalized a states in the C-C backbones, clarifying a long-standing issue in molecular electronics. Our results also substantiate the application of the single-level model for quantitative, unified understanding of transport in benchmark molecular junctions.