This paper presents recent progress towards the development of the EnerCage system for efficient wireless power and data transmission with a focus on its real time control and tracking algorithms. The EnerCage is meant to be used in long-term uninterrupted electrophysiology experiments on small, freely behaving animal subjects in large experimental arenas. It includes a stationary unit for closed-loop inductive power transmission, an array of 3-D magnetic sensors for non-line-of-sight positioning of the animal subject, and a mobile unit to efficiently power the target device and establish wireless data communication. The stationary unit, which includes a scalable array of overlapping hexagonal coils, takes advantage of 3-and 4-coil links to further increase the power transmission efficiency (PTE) and decrease the required number of drivers. A magnetic tracking algorithm is presented that reduces the number of magnetic sensors needed for localization. The algorithm achieves a worst-case localization error of 3 cm at the nominal height of 12 cm above the surface of the coil array. Measurement results show the functionality of the closed-loop power transmission and subject tracking over 70 cm.