So having put the problem on one side for a while and talking to a few people the probable cause for my problems seems to be that the heads have been skimmed beyond the range of adjustment for the manifold gasket and manifold bolts.
It does seem to be a relatively common problem amongst the high performance engine boys.
The pictures show how the gasket overlaps the ports. This is with the end clamps tightened up just to pull the gasket down to roughly where it should be.
So the options I've seen on various sites are:-
Drill out the manifold bolt holes to allow the bolts to line up and trim or cut the gasket in half and rejoin it.
Get the faces of the manifold skimmed to drop it lower.
Get thicker head gaskets.
The problem with 1 is that it seems a bit of a bodge.
The problem with 2 is that the coolant pipe on the manifold is already tight to the gasket.
The problem with 3 is I haven't seen such a thing anywhere.
Very interested to hear everyone's views.