Nonlinear waveguides with two distinct domains of anomalous dispersion can support the formation of molecule-like two-color pulse compounds. They consist of two tightly bound subpulses with frequency loci separated by a vast frequency gap. Perturbing such a two-color pulse compound triggers periodic amplitude and width variations, reminiscent of molecular vibrations. With increasing strength of perturbation, the dynamics of the pulse compound changes from harmonic to nonlinear oscillations. The periodic amplitude variations enable coupling of the pulse compound to dispersive waves, resulting in the resonant emission of multi-frequency radiation. We demonstrate that the location of the resonances can be precisely predicted by phase-matching conditions. If the pulse compound consists of a pair of identical subpulses, inherent symmetries lead to degeneracies in the resonance spectrum. Weak perturbations lift existing degeneracies and cause a splitting of the resonance lines into multiple lines. Strong perturbations result in more complex emission spectra, characterized by well separated spectral bands caused by resonant Cherenkov radiation and additional four-wave mixing processes.