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We scrutinize the paradigm that conventional long-duration Gamma-Ray Bursts (GRBs) are the dominant source of the ultra-high energy cosmic rays (UHECRs) within the internal shock scenario by describing UHECR spectrum and composition and by studying the predicted (source and cosmogenic) neutrino fluxes. Since it has been demonstrated that the stacking searches for astrophysical GRB neutrinos strongly constrain the parameter space in single-zone models, we focus on the dynamics of multiple collisions for which different messengers are expected to come from different regions of the same object. We propose a model which can describe both stochastic and deterministic engines, which we study in a systematic way. We find that GRBs can indeed describe the UHECRs for a wide range of different model assumptions with comparable quality albeit with the previously known problematic energy requirements; the heavy mass fraction at injection is found to be larger than 70% (95% CL). We demonstrate that the post-dicted (from UHECR data) neutrino fluxes from sources and UHECR propagation are indeed below the current sensitivities but will be reached by the next generation of experiments. We finally critically review the required source energetics with the specific examples found in this study.