We theoretically investigate the stochastic decay of persistent currents in a toroidal ultra- cold atomic superfluid caused by a perturbing barrier. Specifically, we perform detailed three-dimensional simulations to model the experiment of Kumar et al. in [Phys. Rev. A 95 021602 (2017)], which observed a strong temperature dependence in the timescale of superflow decay in an ultracold Bose gas. Our ab initio numerical approach exploits a classical-field framework that includes thermal fluctuations due to interactions between the superfluid and a thermal cloud, as well as the intrinsic quantum fluctuations of the Bose gas. In the low-temperature regime our simulations provide a quantitative descrip- tion of the experimental decay timescales, improving on previous numerical and ana- lytical approaches. At higher temperatures, our simulations give decay timescales that range over the same orders of magnitude observed in the experiment, however, there are some quantitative discrepancies that are not captured by any of the mechanisms we explore. Our results suggest a need for further experimental and theoretical studies into superflow stability.