Interference experiments provide a simple yet powerful tool to unravel fundamental features of quantum physics. Here we engineer an RF-driven, time-dependent bilinear coupling that can be tuned to implement a robust 50:50 beamsplitter between stationary states stored in two superconducting cavities in a three-dimensional architecture. With this, we realize high contrast Hong-Ou- Mandel (HOM) interference between two spectrally-detuned stationary modes. We demonstrate that this coupling provides an efficient method for measuring the quantum state overlap between arbitrary states of the two cavities. Finally, we showcase concatenated beamsplitters and differential phase shifters to implement cascaded Mach-Zehnder interferometers, which can control the signature of the two-photon interference on-demand. Our results pave the way toward implementation of scalable boson sampling, the application of linear optical quantum computing (LOQC) protocols in the microwave domain, and quantum algorithms between long-lived bosonic memories.