Thermally induced chain ordering (aggregation) and oxidative damage in neat poly(3-hexylthiophene) (P3HT) films were assessed using multiple optical metrics (low-temperature photoluminescence (LT-PL), Raman, absorbance, and IR spectroscopies) and NMR through quantitative analysis of exciton/chromophore bandwidths, emission, vibronic line shapes, and changes in film chemistry. Polymer morphology is discussed in light of how absorbance and PL provide complementary information about physically and chemically related changes in conjugation due to chain alignment (kinking and torsion), pi-stacking, crystallite domain growth, and photo-oxidation. LT-PL is shown to be sensitive to oxidation phenomena, while absorbance and Raman are not; in contrast, aggregation can be most easily evaluated via absorbance using a Franck-Condon-like model of vibronic excitation. IR and NMR reveal how hexyl side chains and thiophene units are attacked during annealing in O-2. We also demonstrate that competition exists between the "disordering" effect of photodegradation and the physical "ordering" effect of aggregation, each of which dominates under different processing conditions. Ultimately, it is shown that various optical metrics of film disorder must be considered collectively to understand how processing affects film morphology.