Howdy,
You might be interested in my CD FBX Import/Export plugin for Cinema 4D which has the CD Retarget tag. The CD Retarget tag allows you to manually assign joints when the source skeleton is not the same hierarchy as the target skeleton. It also allows you to have multiple source skeletons and switches between the sources with a popup menu.
For this kind of work (using mocap), what I normally do is to create a normal rigged character with IK and constraints, then constrain the IK goals to the controllers instead of parenting them. Then create addition null objects and parent them to a mocap skeleton, and add those objects as targets in the IK goal’s constraints and set up a blend between IK controllers and the mocap targets. This lets the mocap skeleton drive the IK of the rigged character and allows me to blend between manual control and mocap control.
Here is an example video:
http://www.cactus3d.com/bvhBlend.mov
The mocap driver skeleton would then have the CD Retarget tag applied to it, so in the final setup, you’d have the bvh skeleton driving the mocap driver skeleton, which in turn would drive the IK skeleton.
Adios,
Cactus Dan