Trapped-ion experiments are a leading platform for many fields of quantum technology. Most state-of-the-art experiments rely on precise control and characterisation of the ions’ motional state, so improving this area is essential. This thesis presents two novel phonon number measurements: one using the Autler-Townes effect and another using a composite pulse sequence. Additionally, it also presents a spectroscopic investigation of a conformational change of an ion crystal induced by Rydberg excitation. The resulting change in the trapping potential creates a strong coupling between the electronic and vibrational states. This opens new pathways for quantum simulations of molecules. A major challenge in Rydberg ion experiments is double ionisation caused by blackbody radiation. The final part of this thesis offers a solution to this issue by presenting the design of two new cryogenic experiments, one macroscopic and one surface trap.