This Article reports a systematic study on the formation of self-assembled monolayers (SAMs) of conjugated molecules for molecular electronic (ME) devices. We monitored the deprotection reaction of acetyl protected dithiols of oligophenylene ethynylenes (OPEs) in solution using two different bases and studied the quality of the resulting SAMs on gold. We found that the optimal conditions to reproducibly form dense, high-quality monolayers are 9-15% triethylamine (Et3N) in THF. The deprotection base tetrabutylammonium hydroxide (Bu4NOH) leads to less dense SAMs and the incorporation of Bu4N into the monolayer. Furthermore, our results show the importance of the equilibrium concentrations of (di)thiolate in solution on the quality of the SAM. To demonstrate the relevance of these results for molecular electronics applications, large-area molecular junctions were fabricated using no base, Et3N, and Bu4NOH. The magnitude of the current-densities in these devices is highly dependent on the base. A value of beta = 0.15 angstrom(-1) for the exponential decay of the current-density of OPEs of varying length formed using Et3N was obtained.