Automatically reasoning with conflicting generic clinical guidelines is a burning issue in patient-centric medical reasoning where patient-specific conditions and goals need to be taken into account. It is even more challenging in the presence of preferences such as patient's wishes and clinician's priorities over goals. We advance a structured argumentation formalism for reasoning with conflicting clinical guidelines, patient-specific information and preferences. Our formalism integrates assumption-based reasoning and goal-driven selection among reasoning outcomes. Specifically, we assume applicability of guideline recommendations concerning the generic goal of patient well-being, resolve conflicts among recommendations using patient's conditions and preferences, and then consider prioritised patient-centered goals to yield non-conflicting, goal-maximising and preference-respecting recommendations. We rely on the state-of-the-art Transition-based Medical Recommendation model for representing guideline recommendations and augment it with context given by the patient's conditions, goals, as well as preferences over recommendations and goals. We establish desirable properties of our approach in terms of sensitivity to recommendation conflicts and patient context.