Gear whine noise is governed not only by intentional microgeometry modifications but also by unavoidable pitch (indexing) deviation. This study presents a workflow that couples a tooth-resolved surface scan with a calibrated pitch-deviation table, both imported into a multibody dynamics (MBD) model built in MSC Adams View. Three operating scenarios were evaluated—ideal geometry, measured microgeometry without pitch error, and measured microgeometry with pitch error—at a nominal speed of 1000 r min⁻¹. Time domain analysis shows that integrating the pitch table increases the mean transmission error (TE) by almost an order of magnitude and introduces a distinct 16.66 Hz shaft order tone. When the measured tooth topologies are added, peak-to-peak TE nearly doubles, revealing a non-linear interaction between spacing deviation and local flank shape. Frequency domain results reproduce the expected mesh-frequency side bands, validating the mapping of the pitch table into the solver. The combined method therefore provides a more faithful digital twin for predicting tonal noise and demonstrates why indexing tolerances must be considered alongside profile relief during gear design optimization.