Probing electronic wave functions of polyatomic molecules is one of the major challenges in high-harmonic spectroscopy. The extremely nonlinear nature of the laser-molecule interaction couples the multiple degrees of freedom of the probed system. We combine two-dimensional control of the electron trajectories and vibrational control of the molecules to disentangle the two main steps in high-harmonic generation - ionization and recombination. We introduce a new measurement scheme, frequency-resolved optomolecular gating, which resolves the temporal amplitude and phase of the harmonic emission from excited molecules. Focusing on the study of vibrational motion in N2O4, we show that such advanced schemes provide a unique insight into the structural and dynamical properties of the underlying mechanism.