When I down shift from 3rd to 2nd, I can feel a spot where the shift could stay there and be inbetween gears. It is like how neutral feels as you down shift from 2nd to 1st. I make sure that I go through that spot. Could you be stopping the shift too soon?
There is a neutral spot between every gear that can be found if you try.
I can feel the clunk your talking about on my 13 Black.
And have found a neutral between 2nd and 3rd and 3rd and 4th.
Sounds like the design of the tranny could use some help.
All my other Honda's shift very easy and quiet.