A theoretical investigation based on the linear dielectric formalism is presented of the stopping of large clusters in metals at velocities above the Fermi velocity. Calculations are carried out for hydrogen clusters of 4, 13, and 100 H2 molecules stopping in aluminum. Emphasis is placed on the influence of the internal cluster structure, which enters in the present description via the pair-correlation function for the relative positions of nuclei. The target properties are modeled by Lindhard's dielectric function for a free-electron gas. Interference effects with respect to both collective and individual excitations are quantified separately for intra-and intermolecular terms, and are evaluated as a function of cluster velocity. Effects of short-range order, in particular the importance of an exclusion volume around each molecule, are clearly visible. The results indicate, however, that beyond the nearest neighbor the detailed molecular arrangement has only little influence on the stopping power for the clusters studied.