RASAero II, and other rocket software, use the max cross-sectional area of the body as the reference area. In fact in RASAero II the rocket reference area is put on all of the rocket aerodynamic data plots. (Something I think is a good practice.)
Your CD looks like the reference area is the surface area of the rocket. Use the max cross-sectional area of the rocket body as the reference area.
You are attempting CFD analysis where dozens of things can go wrong for a newbie. Since the Cd is off by two orders of magnitude, and you are not even aware that is a problem, tells me you should brush up on the basics before going any further.