The effective conjugation length of the delocalized polymer backbone is one of the key factors in designing monolayer polymers for sensor or nonlinear optical applications. In this manuscript, the photopolymerization behavior of self-assembled diacetylene-containing disulfide monolayers is assessed on gold surfaces. Formation of the long conjugation length, so-called blue form, of the polydiacetylene backbone structure is exclusively monitored using resonance Raman spectroscopy as a function of UV exposure time. In these studies, initial formation of the blue polymer form is followed by an irreversible loss with prolonged exposure. This behavior mirrors the chromatic phase transition to shorter conjugation lengths exhibited for multilayer Langmuir-Blodgett films upon extended UV exposure. Although the exact nature of this phase transition remains elusive, most theories focus on factors affecting the alignment of the polymer backbone and influencing the effective conjugation length. Three such factors are examined here: the Au-S bond with the surface, the crystallinity of the alkyl side chains, and the strain induced by hybridization changes. When the reductive desorption technique is used, the Au-S bond is shown to not be correlated with the polymerization process. In addition, no change in chain crystallinity is observed upon polymerization, but the twist of the methylene chain exhibits significant changes with prolonged UV exposure. This result is consistent with the hybridization-induced strain being translated into the polymer backbone as well as the methylene chains, resulting in a decrease in the effective conjugation length.