Large-scale multidisciplinary design optimization (MDO) of aircraft configurations often considers only a small number of design conditions to reduce computation time and algorithmic complexity. Modern MDO frameworks mitigate derivative-computation complexity by fully automating the assembly of adjoint models. Here, we use a graph-based modeling approach that builds a fine-grained computational graph of the full model, transforms the graph to automatically generate an adjoint model via implicit automatic differentiation, and compiles the graph to JAX for fast execution. With the sensitivity-analysis bottleneck resolved, we address three remaining challenges that arise when scaling MDO to many design conditions. First, we present a differentiable surface mesh deformation strategy that enables smooth updates to the outer mold line (OML) representation, even when aircraft components are independently parameterized and undergo large shape changes. The resulting differentiably morphed OML can drive meshes for solvers of multiple fidelities across many design conditions. Second, we address the memory bottleneck and sensitivity to the initial values of the design variables as the number of design conditions increases. To improve memory scaling and optimization robustness, we propose a distributed MDO algorithm based on block coordinate descent that, unlike existing distributed MDO architectures, is provably convergent to minimizers of the original monolithic MDO problem. Third, given the increasing impact of optimization-algorithm tuning in larger MDO problems, we present two transparent, modular optimizers (OpenSQP and OpenIP) with compact, pure-Python implementations. These algorithms are much easier to tune and customize than existing optimizers, yet they are competitive with and in some cases show improved performance over leading algorithms on the CUTEst test suite. We conclude with a demonstration that combines these methods to solve a large-scale aircraft MDO problem with many design conditions.