This paper presents the design of a low-cost, compact instrumentation system to enable six degree of freedom motion tracking of acetal bricks within an experimental model of a cracked Advanced Gas-Cooled Reactor (AGR) core. The system comprises optical and inertial sensors and capitalises on the advantages offered by data fusion techniques. The optical system tracks LED indicators, allowing a brick to be accurately located even in cluttered images. The LED positions are identified using a geometrical correspondence algorithm, which was optimised to be computationally efficient for shallow movements, and complex camera distortions are corrected using a versatile Incident Ray-Tracking calibration. Then, a Perspective-Ray-based Scaled Orthographic projection with Iteration (PRSOI) algorithm is applied to each LED position to determine the six degree of freedom pose. Results from experiments show that the system achieves a low Root Mean Squared (RMS) error of 0.2296 mm in x, 0.3943 mm in y, and 0.0703 mm in z. Although providing an accurate measurement solution, the optical tracking system has a low sample rate and requires the line of sight to be maintained throughout each test. To increase the robustness, accuracy, and sampling frequency of the system, the optical system can be augmented with an Inertial Measurement Unit (IMU). This paper presents a method to integrate the optical system and IMU data by accurately timestamping data from each set of sensors and aligning the two coordinate axes. Once miniaturised, the developed system will be used to track smaller components within the AGR models that cannot be tracked with current instrumentation, expanding reactor core modelling capabilities.