Digital control systems are traditionally designed independent of their implementation platform, assuming constant sensor sampling rates and processor response times. Applications are deployed to processors that are shared amongst control and non-control tasks, to maximize resource utilization. This potentially overlooks that computing mechanisms meant for improving average CPU usage, such as cache, interrupts, and task management through schedulers, contribute to non-deterministic interference between tasks. This response time jitter can result in reduced system stability, motivating further study by both the controls and computing communities to maximize CPU utilization, while maintaining physical system stability needs. In this paper, we describe an FPGA-based embedded software platform coupled with a hardware plant emulator (as opposed to purely software-based simulations or hardware-in-the-loop setups) that forms a basis for safe and accurate analysis of Cyber-Physical Systems. We model and analyze an inverted pendulum to demonstrate that our setup can provide a significantly more accurate representation of a real system.