That sounds like an interesting project. There's an issue with instancing RailClone objects, including the base objects, as a group because you can't change the parameters of the instances separately (it would affect all objects). The answer could be to try the following.
1 - Create a single RailClone object using X Size, Y Size, or spline Base Objects.
2 - Turn on Free Object, found in the Style rollout. This allows you to move the RailClone object independently of it's base objects.
3 - Instance only the RailClone object, not the base objects. If you want to include this RC object in a Carriage group it shouldn't be a problem.
4 - Link the RC Object or the group containing the RC object to the bone.
Note that you you can't use clipping areas well with this technique because the clipping operation takes place after the object has been moved.
I've attached a simplified sample scene.
I hope that helps, please let me know if you have any further questions.