OK, so no I'm stumped. The noise is 90% better so must be the engine cover but I've still got some noise left and whats left is the same noise...
I've checked the engine cover and its definately fitted properly now.
One thing that did concern me when I refitted the cover was that the foam insulation underneath the cover had pretty much disintegrated. A couple of large pieces were OK but the majority of it was beyond help! It has all come away from the engine cover also. Maybe this is why I still have noise...?