Accurate representation of atmosphere-ocean boundary layers, including the interplay of turbulence, surface waves, and air-sea fluxes, remains a challenge in geophysical fluid dynamics, particularly for climate simulations. This study introduces a stochastic coupled Ekman-Stokes model (SCESM) developed within the physically consistent Location Uncertainty framework, explicitly incorporating random turbulent fluctuations and surface wave effects. The SCESM integrates established parameterizations for air-sea fluxes, turbulent viscosity, and Stokes drift, and its performance is rigorously assessed through ensemble simulations against LOTUS observational data. A performance ranking analysis quantifies the impact of different model components, highlighting the critical role of explicit uncertainty representation in both oceanic and atmospheric dynamics for accurately capturing system variability. Wave-induced mixing terms improve model performance, while wave-dependent surface roughness enhances air-sea fluxes but reduces the relative influence of wave-driven mixing. This fully coupled stochastic framework provides a foundation for advancing boundary layer parameterizations in large-scale climate models.