We have improved our previously described method for extracting activation energies of fragmentation for polyatomic ions from surface-induced dissociation (SID) data [Wainhaus, S. B.; et al. J. Am. Chem. Sec. 1997, 119, 4001]. Our method analyzes the energy-resolved mass spectra and the kinetic energy distribution spectra of the parent and fragment ions that scatter off the surface. It extracts the activation energies by integrating over the distribution of the initial ion energy and the energy transferred to the surface, taking into account both the average value and the width of these distributions. The new method gave improved activation energies for SiMe3+ --> SiMex+ (x = 0-2) fragmentation at a hexanethiolate-covered gold surface. We then used our data analysis method to analyze the activation energies for the fragmentation of thiophene ions at the hexanethiolate-covered gold surface. The activation energies for the formation of C2H2S+, CHS+, and C3H3+ from C4H4S+ were found to be 4.6 +/- 0.7, 6.9 +/- 0.7, and 6.5 +/- 0.7 eV, respectively. Our activation energy results followed the trend in the values from threshold photoelectron photoion coincidence data. However, the SLD values were similar to 50% higher than the threshold photoelectron photoion coincidence values; this discrepancy mostly resulted from delayed dissociation. This model may be used to extract quantitative activation energies from SID data once certain ongoing issues are resolved in future papers. Molecular dynamics simulations were also performed to assist in the data analysis and to test the assumptions of energy transfer in this system. Qualitative agreement in energy transfer was found between the experiments and simulations.