Ongoing Xiahou Ba Rigging Failures

Bare in mind before reading this, this is the 3rd time I've pretty much typed this issue out trying to get help to fix it from Polycount and Area forums.

The issues are less than when I previously posted thankfully, however they are still far from correct. 

The stage I am at now is simply putting the motion capture skeleton into T-pose to match my characters pose, keyframed on frame -1 so that it doesn't affect the data in any way. This T-posed version is the duplicated to make sure both rigs are exactly the same, but of course the duplication does not keep its keyframed animation data.

Using Maya's built-in HumanIK system for retargeting animation data, I create a new skeleton rig for each skeleton. Then you simply tell the character's skeleton (the duplicate), to follow the original motion capture skeleton as a source of data. This works, but goes very wrong.

Above shows both the original and duplicate rig on top of one another. I have also told the major joints to show their local rotation axis to show that they are set up correctly and are both identical to one-another. You can also see HumanIK believes there to be no problems with either skeleton.

Above here shows you what happens when I tell my character's skeleton to follow the motion capture data. The skeleton of my character becomes all bent out of shape. Below shows you a better rendition of what is going wrong here:

This is very frustrating. The issues looks like it must be caused by a difference in joint rotation between the two skeletons, but there isn't one. I'm not sure why the skeleton moves its root (pelvis bone) up a bit from where it should be too, or why the wrists are bending when the animation is played instead of the elbows as they are on the motion capture data. Both skeletons are set up anatomically correctly in the HumanIK editor, so surely this should not happen either.

All I can do is wait for someone with better knowledge in this to get back to me and hope its a simple fix. So close, yet so far.... I must be missing something really silly!