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Pharmaceutical and high-speed manufacturing environments increasingly require digital systems that can connect physical production activities with real-time process control, traceability, quality assurance, and regulatory compliance. This paper presents Project GEMINI, a custom Manufacturing Execution System (MES) and Electronic Batch Record (EBR) transformation designed to integrate complex manufacturing operations into a unified digital execution platform. The study focuses on the architectural translation of physical production workflows into executable digital instructions covering material dosing, supersack-to-Intermediate Bulk Container (IBC) conversion, sequential in-bin blending, secondary ingredient addition, case coding, robotic palletization, pallet identification, and automated quality inspection.The custom EBR was designed not merely as an electronic replacement for paper records but as an active manufacturing-control layer capable of guiding operators, enforcing process sequences, recording critical events, and maintaining traceability throughout production. Integration with X-Ray and Vision inspection systems enabled physical quality decisions to be synchronized with electronic records, while integration with Oracle EBS R12 established enterprise-level material, inventory, and production information exchange. The resulting architecture created a digital lineage, referred to in the project as a "Golden Thread," connecting raw-material lots, manufacturing activities, equipment, operators, quality events, and finished pallets.A stakeholder-centered implementation methodology was used through Functional Walkthroughs, Conference Room Pilots (CRPs), User Acceptance Testing (UAT), iterative gap analysis, and GxP-oriented validation. Reported outcomes included a 20% increase in production throughput, 30% improvement in sanitation efficiency, approximately 25% reduction in plastic waste, 1–3% material-yield recovery, improved dispensing accuracy, and mitigation of potentially multi-million-dollar product-recall exposure. The architecture also established a Digital Birth Certificate for finished pallets, supporting end-to-end traceability and regulatory readiness. The findings demonstrate that a custom MES/EBR can provide value beyond production-data capture by functioning as an integrated digital control layer between operators, automated equipment, quality systems, and enterprise applications.