The switching of single cyclooctadiene molecules chemisorbed on a Si(100) surface between two stable conformations, can be achieved with a scanning tunneling microscope [Nacci et al., Phys. Rev. B 77, 121405(R) (2008)]. Recently, it was shown by quantum chemical and quantum dynamical simulations that major experimental facts can be explained by a single-mode model with switching enforced by inelastic electron tunneling (IET) excitations and perturbed by vibrational relaxation [Nacci et al., Nano Lett. 9, 2997 (2009)]. In the present paper, we extend the previous theoretical work in several respects: (1) The model is generalized to a two-mode description in which two C(2)H(4) units of COD can move independently; (2) contributions of dipole and, in addition, (cation and anion) resonance-IET rates are considered; (3) the harmonic-linear vibrational relaxation model used previously is generalized to anharmonic vibrations. While the present models highlight generic aspects of IET-switching between two potential minima, they also rationalize specific experimental findings for COD/Si(100): (1) A single-electron excitation mechanism with a linear dependence of the switching rate on tunneling current I, (2) the capability to switch both at negative and positive sample biases, and (3) a crossover temperature around ~60 K from an IET-driven, T-independent atom tunneling regime, to classical over-the-barrier isomerization with exponential T-dependence at higher temperatures for a bias voltage of +1.5 V and an average tunneling current of 0.73 nA.