This paper describes a method of fabrication that generates small arrays of tunneling junctions based on self-assembled monolayers (SAMs); these junctions have liquid-metal top-electrodes stabilized in microchannels and ultraflat (template-stripped) bottom-electrodes. The yield of junctions generated using this method is high (70-90%). The junctions examined incorporated SAMs of alkanethiolates having ferrocene termini (11-(ferrocenyl)-1-undecanethiol, SC(11)Fc); these junctions rectify currents with large rectification ratios (R), the majority of which fall within the range of 90-180. These values are larger than expected (theory predicts R <or= 20) and are larger than previous experimental measurements. SAMs of n-alkanethiolates without the Fc groups (SC(n-1)CH(3), with n = 12, 14, 16, or 18) do not rectify (R ranged from 1.0 to 5.0). These arrays enable the measurement of the electrical characteristics of the junctions as a function of chemical structure, voltage, and temperature over the range of 110-293 K, with statistically large numbers of data (N = 300-800). The mechanism of rectification with Fc-terminated SAMs seems to be charge transport processes that change with the polarity of bias: from tunneling (at one bias) to hopping combined with tunneling (at the opposite bias).