Recent experiments have been able to measure the conductance of individual molecules by repeatedly raising and lowering a gold plated AFM tip into a self-assembled monolayer on a gold substrate. Upon raising the tip after it has formed several metal-molecule-metal junctions and recording the current simultaneously, the experiments reveal descending steps in the trace which indicate the detachment of individual junctions until a single molecular conductance is isolated. Interesting fluctuations in these steps indicate changes in the molecular conductance with stretching. We report theoretical calculations which employ a local orbital DFT code for a candidate molecule with varying degrees of stretching. An efficient, self-consistent transfer matrix program is then used to determine the conductance as the molecule is stretched. Conductance peaks are observed despite the increased tunneling distance indicating an enhanced coupling of extended gold states in the contacts to the molecular states. Two different molecules are examined in order to compare the influence of molecular planarization on the conductance behavior.