So far almost everything has been linked up. The last few elements required are the fins. As I found the IK control system quite handy, I decided that barring other suggestions I use that to make controlling the fins easier, as I had to get rid of a few controls for the old method when rebuilding the neck.
There was some minor warping when I linked up the blendshapes to the model, but a loophole I found to reduce the severity was to reduce two of the shapes - one for the lips and around the eyes, one for the cheeks, are working at half-strength. While this does mean their controls need to be moved further for a better effect, it seems like a worthwhile compromise.
The counter-roll for the spine's IK also works effectively. However since copying the rotation for the core joint overshoots the counter-rotation it might have to be controlled on a by-eye basis.