We carefully validated our computational model regarding the dispersion correction, supercell and k-mesh sizes, and stacking order. After investigating several dispersion models, we conclude that the choice of dispersion model must be made with great care, which very likely is also true for other layered materials. We observed that the TS correction, unlike most other models, yields a physically sound PES for COF-1, resulting in well-preserved layer stackings throughout the AIMD simulation. Furthermore, our findings indicate that the stacking order influences the width and intensity of certain peaks. We recommend using a supercell rather than a k-mesh setup to account for stacking disorder between nonadjacent layers, as found in a recent previous study. We assessed different methods to compute dipole moments and polarizability tensors and their effect on AIMDbased IR and Raman intensities. We found that Berry phase dipole moments and DFPT polarizabilities yield the best agreement with experiment for the overall IR and Raman spectra, respectively. We also demonstrated that MLWFs can be used to analyse and dissect the AIMD-computed spectra into contributions from individual molecular building blocks and chemical bonds. This approach can possibly be used in in situ monitoring of reactions of other porous materials which form via bimolecular mechanisms, since it allows tracking the formation of the bonds connecting the reactants.