tried to open your zips but they are corrupted. i can see the fbx inside but it doesn´t let me extract the file.
anyway. make sure before your feed your mocap skeleton into your own skeleton that you have an idential T-pose on your very first frame in MB with both skeletons. maybe that´s what went wrong in the beginning. I had the same prob once. ever after I use the same mocap skeleton as start for my skinned skeleton.
what I else want to tell you is - I am working with MB for a month now and like you I keep jumping from the hot pan into the fire each time a problem is solved. I also didn´t find any apparently experienced community for MB yet like we have it here at simplymaya. simplymaya rocks! I know now more than ever before.
if you have any good ressources on how to handle mocapData with layered animation, please m8! let me know! I have a feeling like we are in kind of a same situation.
everything starts and ends in the right place at the right time.