The attenuation corrections factors (ACFs), which are necessary for quantitatively accurate PET imaging, can be obtained using singles-mode transmission scanning. However, contamination from scatter is a largely unresolved problem for these data. We present an extension of the Monte Carlo simulation tool, GATE, for singles-mode transmission data and its validation using experimental data from the microPET R4 and Focus 120 scanners. We first validated our simulated PET scanner for coincidence-mode data where we found that experimental resolution and scatter fractions (SFs) agreed well for simulations that included positron interactions and scatter in the source material. After modifying GATE to model singles-mode data, we compared simulated and experimental ACFs and SFs for three different sized water cylinders using 57Co (122 keV photon emitter) and 68Ge (positron emitter) transmission sources. We also propose a simple correction for a large background contamination we identified in the 68Ge singles-mode data due to intrinsic 176Lu radioactivity present in the detector crystals. For simulation data, the SFs agreed to within 1.5% and 2.5% of experimental values for background-corrected 68Ge and 57Co transmission data, respectively. This new simulation tool accurately models the photon interactions and data acquisition for singles-mode transmission scans.