Howdy,
One of the problems with applying motion capture to a rigged character is that the imported motion capture skeleton may not have the same joint twists as the skeleton to which the mesh is bound.
The easiest ways to handle it is to create 2 joint skeletons for the character. One rigged normally with IK and constraints, etc., to which the mesh will be bound, and the second skeleton to be used as a driver skeleton for the first one. What I mean by “driver” skeleton is that within that second skeleton, parented to specific joints will be target nulls to which the IK goals can be targeted, so that the second skeleton can drive the IK of the first skeleton.
You would then retarget the motion of the imported mocap skeleton to the driver skeleton, which will in turn drive the IK skeleton.
Here is an example of a driver skeleton driving an IK skeleton with a blend between the 2:
https://www.cactus3d.com/bvhBlend.mov
… and an example with a bound mesh:
https://www.cactus3d.com/bvhExample2.mov
It takes a little work to get the initial rig set up with the IK and driver skeletons, but once that is done, that can be your standard rig from there on out.
Adios,
Cactus Dan
Cinema 4D R13 Prime
http://www.cactus3d.com
http://www.cactus3d.com/Plugins.html