This is EXACTLY the same noise I posted on here a week or so ago. It stops when the clutch is fully down. It can only be input shaft on the gearbox since its the only thing that stops turning when the clutch is fully pressed (the release bearing et all still spins.

I spoke to a specialised MX5 gearbox rebuilders and they told me that the Mk2 box is known for it and is "normal" (the Mk2 box has the hidden gear selector shaft the Mk1 is exposed). Since no-one will warranty a Mazda box in a Morgan Im just going to leave it and enjoy it till it gets really bad then stick a second hand box in it - they are throwing them away as they last longer than the rusty Mazdas

Currently at 40,000 miles - noticed it around 30,000, I have changed the oil and ran a magnet through the drained oil and no metal at all, virtually none on the drain plug so perhaps it is normal!