Whilst cleaning up shot 25 to be used as a master scene, I linked all the textures for the eel and then noticed that the glowing orbs were not connected to the rig, nor were they even in the scene. I got quite concerned so they are a big part of how the viewer is going to identify the eel, and mentioned this to Andy. We then called Clym and asked if he had attached those orbs to the mesh, and he said he had not. It was then a case of how to rectify this, and he suggested using the wrap deformer, to attach the orbs to the main body, as they would then follow the mesh.
So what has to be done for all shots including the eel is to manually import the orbs, and then connect them to the existing mesh using the wrap deformer. It is an easy fix, however quite tedious, as I began with shot 25. I had to go in and manually move each orb to the mesh, then attach. Its going to be worth it in the end :)