I am happy that the reviewer comments have been largely addressed. However:

1. In your response to referee 2 point 19 you add further discussion of the relaxation flux. You may wish to consider adding some of this discussion to the text.

I also have the following minor comments:

2. Page 19 line 20: Please clarify "course-resolution" -- I believe this refers to "coarse-resolution fixed mesh"?
3. Figure 19: Do the colour scales refer to layer thickness rather than height?
4. Page 29 lines 18-19: I do not understand the revised text. Why should a stronger stratification weaken the diffusivity? Please consider rephrasing.
5. Page 29 line 25: I find this sentence to be a little ambiguous -- is this opposite to the direction of the wind, or opposite to the direction reported in Verburg et al. (2011)? Please consider rephrasing.

and also:

Page 9 line 1: "Coriolis parameter" is the more common terminology here.
Page 9 lines 9-10: Please complete the reference which appears here (the year is missing?).
Page 9 line 23: please clarify the final part of this sentence, "but there are written for $\Omega_t$".
Page 2 line 22 "an r-adaptive", page 30 line 15: "on"->"in".

The colour scale of figure 19 still refers to the "Level height", which I think should be "Level thickness".