You absolutely can link a puppet pin to a Null Object, so there’s that. You also have the problem of the head moving and needing the puppet pin to move, but only distort at key points.
So…
How about precomping a copy of footage to stabilise the shot on the animal’s head. This will keep it fixed. You can then add the puppet pins to the precomp layer. Each puppet pin will give you an X and a Y coordinate. You could use an expression to drive the distortion of the mouth using audio?
For my tutorial character, I use Adobe Character Animator. I use a basic mouth, drop my audio in, get CA to do the lip sync-ing, then use the Copy Visemes to After Effects option. This gives me a bunch of keyframes I can paste onto a property. In my case, I have a precomp of mouth shapes and paste onto Time Remapping to get the mouth to sync up. But in your case, it might be just as easy to paste onto a slider, then use something like this expression on your pin:
X=value[0];
Y = value[1]-effect("Slider Control")("Slider");
[X,Y];
Now – the other thing you could use Character Animator for is capturing other facial movements. Sit infront of a webcam while playing the audio and CA will give you keyframes for each head tilt etc… you could even use Photoshop to help recreate your animal heads in CA, render everything out there, then bring the animated head into AE for tracking onto the animals.
http://www.YouTube.com/ShiveringCactus – After Effects Tutorials