The reconstruction of large protein assemblies is a major challenge due to their plasticity and due to the flexibility of the proteins involved. An emerging trend to cope with these uncertainties consists of performing the reconstruction by integrating experimental data from several sources, a strategy recently used to propose qualitative reconstructions of the Nuclear Pore Complex. Yet, the absence of clearly identified canonical reconstruction and the lack of quantitative assessment with respect to the experimental data are detrimental to the mechanistic exploitation of the results. To leverage such reconstructions, this work proposes a modeling framework inherently accommodating uncertainties, and allowing a precise assessment of the reconstructed models. We make three contributions. First, we introduce toleranced models to accommodate the positional and conformational uncertainties of protein instances within large assemblies. A toleranced model is a continuum of geometries whose distinct topologies can be enumerated, and mining stable complexes amidst this finite set hints at important structures in the assembly. Second, we present a panoply of tools to perform a topological, geometric, and biochemical assessment of the complexes associated to a toleranced model, at the assembly and complex levels. At the assembly level, we track the evolution of complexes and their stoichiometry. At the complex level, we present tools to compare a complex against a predefined 3D template, in terms of protein instances and pairwise contacts. Third, we apply our machinery to the NPC, thus bridging the gap between the aforementioned global yet qualitative models, and atomic-resolution models of sub-complexes. These contributions should prove instrumental in enhancing the reconstruction of assemblies, and in selecting the models which best comply with experimental data.