Charge transfer doping efficiencies of pi-stacked poly(3-hexylthiophene) (P3HT) aggregate nanofibers are studied using spectroscopic and electron microscopy probes. Solution dispersions of self-assembled P3HT nanofibers are doped in the ground electronic state by adding varying amounts (w/w%) of the strong charge transfer dopant 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F-4-TCNQ). Careful control of self-assembly conditions allows us to select either the H- and J-aggregate limiting forms, which differ primarily in the degree of purity (i.e., molecular weight fractionation) and nanomorphology. Electron paramagnetic resonance (EPR), electronic absorption, and Raman spectroscopy of F-4-TCNQ(-):P3HT+ species are then used to track doping efficiency with dopant loading. J-aggregate nanofibers exhibit over an order of magnitude larger doping efficiencies than polymorphic H-aggregate nanofibers. The higher purity and order of the former promote intrachain polaron delocalization whereas disorder arising from greater molecular weight polydispersity in the latter instead lead to polaron localization resulting in charge transfer complex formation. Interestingly, J-aggregate nanofiber EPR signals decrease significantly after similar to 25% F-4-TCNQ loading which we attribute to increased antiferromagnetic coupling between delocalized hole polarons on neighboring P3HT chains leading to spinless interchain bipolarons. Raman spectra excited on resonance with NIR F-4-TCNQ(-):P3HT+ absorption transitions also reveal quinoid distortions of the P3HT backbone in J-aggregates. We propose that self-assembly approaches to control aggregate packing and purity can potentially be harnessed to achieve long-range, anisotropic charge transport with minimal losses.