Hi Gaz... just had a look at your setup - very nice indeed
if you take a look at the attached file (btw this is mostly in reference to your original prob) you'll hopefully find everything is ok, though I cant promise anything as I'm really hungover (office party last night ).
As you'll see theres a new root node, and the clusters and head locator are parented and move properly with the rest of it. The reason everything was getting screwy was because of the deformation order. If you selct the mesh, then click on "Inputs to the selected object" (next to the magnet) and from that list click All Inputs..
Then move the skin cluster entry up to the top of the list. You'll probably need to do the same with blend shapes too..
hope this helps mate