Dear Rwoolhou, 
The solution of cell zone separation might work for simple geometries (Tried it, worked), but impossible for the real application (See 8th post from the top).

Is there a chance to upload the geometry somewhere private to get your (or other colleagues') comment on it? I am not allowed to publicly share the case.

May I also add another moderator to this talk? I would be pleased to involve Peteroznewman to this loop please.