The electro-mechanical system (EMS) is becoming increasingly complex and sensitive to damage during assembly and integration. Such risks are increased by compressed development cycles and strict cost constraints. In addition, EMS comprises numerous sub-components, each exposed to significant supply chain risks. Key challenges include long lead times and limited sourcing options for essential components, such as complex printed circuit board assemblies (PCBAs), electronic components, and processor modules. To address these challenges, an efficient design process should reduce design iterations and facilitate assembly decisions early in development. Data-driven concurrent design and tolerance analysis are essential to ensure system reliability and manufacturability. To achieve this, we propose a Risk-Prioritized Digital Twin (RPDT) framework for the concurrent development of design and assembly processes. The RPDT framework integrates three key components: failure modes and effects analysis (FMEA), visual kinematic simulation, and tolerance analysis. FMEA is initially used to prioritize high-risk components and processes for RPDT application. By combining tolerance analysis and visual kinematic simulation, the RPDT framework enables early-stage risk detection and quantification through the superposition of static design tolerances and kinematic process parameters. An industry case study demonstrates the application of this framework to system hardware development for a high-density server. The results show that the RPDT framework reduces physical build iterations, minimizes material waste, and prevents costly soft-tooling and prototyping cycles.