You are using manual edit cross sections to create rectangles. This introduces two problems.
1) They still have the problem that the sides collapse flat when running in VLM mode.
2) Unless you adjust the U_i values around your curve, the loft lines will not connect the corners together. This can lead to some very strange feature lines that your model exhibits. This will also be reflected in the mesh quality -- which will be very odd when smashed to VLM.
Control surface deflection currently only works in VLM mode. So, you'll want to resolve all the above problems. You will need more spanwise resolution for your model.
If you really want the fuselage included in your VLM, then I would change the cross sections to ellipses with the same width and height.
If it were me, I would just drop the fuselage and use the wing and tail combination for your purposes. I would also drop the small cockpit blister on top of the fuselage.
For other purposes, you may still want the fuselage in the model -- I would switch the cross sections to rounded rectangles with zero radius corners. Keep the 'Key Corner' button 'on' and it will connect the corners together in a nice way.
Rob