Demand for using data analytics for energy management in buildings is rising. Such analytics are required for advanced measurement and verification, commissioning, automated fault-detection and diagnosis, and optimal control. While novel analytics algorithms continue to be developed, bottlenecks and challenges arise when deploying them for demonstration, for a number of reasons that do not necessarily have to do with the algorithms themselves. It is important for developers of new technologies to be aware of the challenges and potential solutions during demonstration. Therefore, this paper describes a recent deployment of an automated, physical model-based, FDD and optimal control tool, highlighting its design and as-operated benefits that the tool provides. Furthermore, the paper presents challenges faced during deployment and testing along with solutions used to overcome these challenges. The challenges have been grouped into four categories: Data Management, Physical Model Development and Integration, Software Development and Deployment, and Operator Use. The paper concludes by discussing how challenges with this project generalize to common cases, how they could compare to other projects in their severity, and how they may be addressed.