Well now, here's a surprise. While the engine / gearbox was out on the bench I changed the gearbox oil. I used bog standard 75/85 mineral oil as recommended by MX5ers and the noise is gone. Not just quieter but gone - you can't tell from the sound wether the clutch is engaged or not. Don't know what to make of this but Draggin, take note.
Phil: this is probably a dumb question but where on the gear box is the fill hole?