Rigging to a .bvh file

When importing .bvh files they show the movement captured from the mocap, that's fine, but to get it to rig to a character is where the real challenge lies. Obviously I already have my mesh from the tutorial so I tried to use my previous 'walk' file.

I imported the file as an armature, and rotated it to stand alongside my already rigged character. I then scaled him down to get them to the same shape etc.

I changed the armature constraint to track to the new armature 'mocap_arm' and then weight painted one of the bones and this happened! It does move when I run it along the timeline, but it is placed completely wrong.


I then weight painted everything, just to check that it still formed the mesh's shape, which it did.

But of course it would not move as the motion did because it was all following the right upper arm. The black lined armature and eyes is what I used before, I've not rectified/removed this yet, which may be part of the problem?

I thought putting the armature into rest mode and changing the position and length of bones so I put the x mirror modifier on and it jumped out like this...?