Pair Distribution Function (PDF) analysis of molecular materials often requires complex multi-phase models that mix crystalline and molecular components with distinct displacement parameters. We present recent developments in HighScore v6.0 that streamline molecular PDF analysis for functional materials. A central advance is the ability to automatically identify complete molecular units directly from crystal structures, even when a molecule extends across multiple neighboring unit cells, eliminating manual reconstruction steps that previously limited throughput and reproducibility. This is achieved through a set of generic, molecule-centric PDF scripts that automatically prepare and constrain three-phase P1 models, a crystalline reference phase together with “sharp” and “broad” molecular phases, generated and sorted based on atomic counts and Biso signatures. These scripts implement automated sanity checks, atom mapping, and constraint generation, enabling simultaneous refinement of molecular positions across all phases without manual intervention. Integrated into the broader HighScore v6.0 automation framework, these workflows leverage improved scripting and abstraction layers designed to hide unnecessary complexity and ensure reproducibility across large data series. The result is a significantly simplified PDF setup for molecular systems, reduced user overhead, and more robust modelling of functional materials exhibiting mixed local order. These developments support high-throughput total-scattering studies and provide a foundation for future automated and data-driven PDF analysis extensions.