This paper investigates the interference effects of wind tunnel floor and walls on the Japan Aerospace Exploration Agency’s High-Lift Configuration Standard Model (JSM) as an extension to a paper published in the Journal of Aircraft, Vol. 56, No. 3, May–June 2019, pp. 1080–1098. An unstructured hybrid grid generator, MEGG3D, was applied to JSM wing–body and wing–body–nacelle–pylon configurations to generate grids for free-air flow conditions. These grids were then reused in an investigation of the interference effects of Japan Aerospace Exploration Agency’s low-speed wind tunnel walls to better compare the computational results, both with each other and with experiment. The geometry of the wind tunnel used in our computational simulations is described in detail so that they can be reproduced. A Reynolds-averaged Navier–Stokes flow solver for unstructured hybrid grids, the Tohoku University Aerodynamic Simulation (TAS) code, was used for the simulations. The computational results indicated that the standoff and test section floor boundary layer significantly affected the aerodynamics of the JSM at high angles of attack. Better agreement with experiment was observed for the wing–body configuration in the aerodynamic characteristics near maximum lift if the effects of the standoff and floor boundary layer were considered.