Spin defects in diamond serve as powerful building blocks for quantum technologies, especially for quantum sensing and networking. Electron-nuclear defects formed near optically active spins such as the nitrogen-vacancy center provide a resource for multi-qubit quantum registers. However, many remain uncharacterized, limiting their control and integration in quantum devices. Here, we identify the hyperfine components, including their relative sign, and nuclear spin species of two unknown dark spin defects using zero-field double electron-electron resonance spectroscopy and a protocol based on electron-nuclear double resonance. New ab initio calculations assign one defect to a known nitrogen interstitial, while the hydrogen-related defect matches no calculated or previously reported structure. We further use this protocol to demonstrate initialization, unitary control, and long-lived coherence of the hydrogen nuclear spin qubit, with a coherence time of 1.0(3) ms. These characterization and control tools establish a framework for harnessing unknown electron-nuclear defects for quantum registers.