I am not saying that you should zero out the wing and tail locations -- I merely did that as an expeditious way of comparing to your hand calcs (which I assumed ignored z-components). The z-effect is real, but for many aircraft it is small and can be ignored. That may not be the case for your aircraft.
You can use whatever CG location you want as your moment center location -- just be sure to use the same location in VSPAERO as in your hand calcs. You really shouldn't be focused on the static margin right now. Instead, it is probably better to think about calculating the location of the aerodynamic center.
Once you reach confidence in your calculation of the aerodynamic center, you can then back-calculate a desired CG location to give the static margin that you want. Then you arrange the components of the aircraft to get the CG as close to the desired location as possible. Finally, you add ballast to fix whatever went wrong.
If you want to get a little more complex, you can look at moving your wing along the fuselage as you size the tail and elevator. When you do so, you need to look at your landing gear position as well -- consider tip-back angle, pitch stability, elevator authority, load on the nose wheel, etc. Depending on your vehicle, you'll need to look at forward and aft cg locations too.
When calculating cl_alpha in your hand calculations, are you using any form of aspect ratio correction -- or are you just using 2*pi per radian or 0.1 per degree?
Rob
Thanks for the help and suggestions Rob.
Making those changes and including the fuselage, I get an SM of 35% (5% less than previous result).
As you noticed, I am using the desired cg location in VSPAero as my datum... should I be using a different datum? Also, the wing's Z_displacement value is not zero because I choose my fuselage to be at (0,0,0) and the wing is displaced upwards in referenced to the fuse. I dont think I can do much in zeroing out the wing's Z_location, unless I shifted all other aircraft components down... but as you said, that zeroed Z_location of the wing had a significant effect on SM...
I'll keep digging and see if I made a mistake in my hand computations. I did ignore the z-components of everything...
Thanks.