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Numerically addressing scientific questions such as simulating drug diffusion through the human stratum corneum is a challenging task requiring complex codes and plenty of computational resources. The UG4 framework is used for such simulations, and though empirical tests have shown good scalability so far, its sheer size precludes analytical modeling of the entire code. We have developed a process which combines the power of our automated performance modeling method and the workflow manager JUBE to create insightful models for entire UG4 simulations. Examining three typical use cases, we identified and resolved a previously unknown latent scalability bottleneck. In collaboration with the code developers, we validated the performance expectations in each of the use cases, creating over 10,000 models in less than a minute, a feat previously impossible without our automation techniques.