Understanding the roles of disorder and metal/graphene interface on the electronic and transport properties of graphene-based systems is crucial for a consistent analysis of the data deriving from experimental measurements. The present work is devoted to the detailed study of graphene nanoribbon systems by means of self-consistent quantum transport calculations. The computational formalism is based on a coupled Schrödinger/Poisson approach that respects both chemistry and electrostatics, applied to pure/defected graphene nanoribbons (ideally or end-contacted by various fcc metals). We theoretically characterize the formation of metal-graphene junctions as well as the effects of backscattering due to the presence of vacancies and impurities. Our results evidence that disorder can infer significant alterations on the conduction process, giving rise to mobility gaps in the conductance distribution. Moreover, we show the importance of metal-graphene coupling that gives rise to doping-related phenomena and a degradation of conductance quantization characteristics.