So after having a little fiddle with the rig, i realized that when i imported my character into the MayaLive scene it was too big, and i had no way of successfully scaling him down to fit the scene.
When i'd try and import him in with different scale settings the rig wouldn't resize with the mesh, also the problem i had with the left ear means when i re combine the mesh to the rig the ear spins in on itself. All crazy business.
So as it's being close to the deadline, i have decided to just admit defeat on JP and bring in another rig, which is a little baby dinosaur. I chose this dinosaur because the rig scales, it's a simple rig and i wanted to have a bi pedal rig as this was what JP was.
I have had a play with the dinosaur rig and all seems to work as i want it to.
So now i have the five scenes to animate on top of, and i've tested the dinosaur with the tracking, all works well. TICK TOCK!