Superconducting radio frequency (SRF) cavities provide an excellent platform for storing quantum information as quantum $d$-level systems (qudits) due to their exceptionally long lifetimes and large accessible Hilbert spaces. A common strategy to manipulate the states is to use a nonlinear element like a transmon. There are, however, several challenges to building a 3D SRF architecture while maintaining a long cavity lifetime. We demonstrate our successful integration of transmons with single-cell Nb SRF cavities and the ability to prepare several non-classical states. Finally, we discuss our strategies to improve the coherence times, gate schemes, and extend the system for building a multi-qudit quantum processor.