Spin-coated poly(9,9-di-n-octylfluorene-alt-benzothiadiazole) (F8BT) films of different molecular weights (M-n = 9-255 kg/mol), both in the pristine and annealed state, were studied in an effort to elucidate changes in the polymer packing structure and the effects this structure has on the optoelectronic and charge transport properties of these films. A model based on quantum chemical calculations, wide-angle X-ray scattering, atomic force microscopy, Raman spectroscopy, photoluminescence, and electron mobility measurements was developed to describe the restructuring of the polymer film as a function of polymer chain length and annealing. In pristine high molecular weight films, the polymer chains exhibit a significant torsion angle between the F8 and BT units, and the BT units in neighboring chains are close to one another. Annealing films to sufficiently high transition temperatures allows the polymers to adopt a lower energy configuration in which the BT units in one polymer chain are adjacent to F8 units in a neighboring chain ("alternating structure"), and the torsion angle between F8 and BT units is reduced. This restructuring, dictated by the strong dipole on the BT unit, subsequently affects the efficiencies of interchain electron transfer and exciton migration. Films exhibiting the alternating structure show significantly lower electron mobilities than those of the pristine high molecular weight films, due to a decrease in the efficiency of interchain electron transport in this structure. In addition, interchain exciton migration to low energy weakly emissive states is also reduced for these alternating structure films, as observed in their photoluminescence spectra and efficiencies.