How to position/scale custom bone shapes in same position as original mesh? I'm trying to make some custom bone shapes for my armature control bones. I've made the custom shapes in the location I want. However, whenever I set the 'Display -> Custom Shape' property to the object I made, it appears in a crazy orientation and scale relative to the bone's position (not in the position of the 'real' mesh, as I'd expect).
I've applied the rotation and scale to the original mesh I want to use as the shape (using CtrlA) but am unable to get it to work in place like I'd expect. 

I've read that the bone size and orientation are applied to the mesh shape key (I'm assuming the size and rotation relative to the parent?). That seems like it's terrible, is there some way to turn it off or position the original mesh so it lines up?

I found a plugin ( http://wiki.blender.org/index.php/Extensions:2.6/Py/Scripts/Rigging/Auto_custom_shape ) that seems to do what I want - but it doesn't seem to work with the newer version of blender I'm using (2.73).

I don't want to just randomly flip and scale my original mesh around in the scene until it looks right - that seems like it's just going to be confusing down the road if I need to change the shape (as it will be in an arbitrary orientation in the scene someplace). There has to be a way to set this up nicely - I can see that rigify puts it's WGT-* bone shape meshes in the world in a way that lines them up with the bones they're applied to.

Anyone have a good solution for this?
For solving this issue I use a script called orient_custom_shape_V2.py I found here:
https://developer.blender.org/F207430

After installing and activating the script in User Preferences select a custom shape as you do normally (Pose Mode -> Bone panel -> Display section). Then you have this new button called Orient Custom Shape beneath the custom shape options. It should bring the representation of your bone to where your custom shape mesh is. Which is what we want.



It works fine for me (v.2.77). Though I know people experienced issues with scale and orientation for some bones using the script.

And as to scale I recommend having bone size equal to one if possible (this should not scale your custom shape at all).