The objective of this paper is to understand the effects of waves and vaporous cavitation upon the hydrodynamic and hydroelastic responses of a flexible surface-piercing hydrofoil, adding to the subcavitating results presented in Part 1. In general, the presence of a sufficiently large vaporous cavitation bubble facilitated the formation of a ventilated cavity, substantially reducing the angle of attack or speed required to induce fully ventilated flow, relative to subcavitating conditions. A new co-analysis procedure was used to isolate synchronous hydrodynamic modes and structural operating deflection shapes. Significant dynamic load amplification occurred when the resonant frequencies of the first twisting and second bending modes coalesced in both fully wetted and partially cavitating flows. The presence of waves did not diminish the effect of frequency coalescence, but did encourage intermittent lock-in with both leading edge cavity shedding and trailing edge vortex shedding at certain speeds. Partial cavity shedding typically had a negligible impact on the power spectral densities of structural motions because of incoherent cavity shedding. However, lock-in between the cavity shedding frequency and modal coalescence frequency led to shifting of the primary frequency peak, as well as amplified harmonics and interactions between the cavity shedding frequency and vortex shedding frequency. The transition from partially cavitating to fully ventilated flow caused sudden and large drops in the mean hydrodynamic loads and deformations, as well as substantial reductions in the intensity of the fluctuations.