Suggested improvements:
a) Layers 36-41 are zero thickness everywhere. So you could run with 35 layers and save about 15% of the computer time. In principle the extra layers do no harm, although I see some zero salinity artifacts in these layers occasionally.
b) There is negative salinity at the surface:
157441083 i,j,k = 268 110 1 neg. saln after advem call -0.01
157441086 i,j,k = 276 78 1 neg. saln after advem call -0.01
I think this is due to too-strong river forcing. I suggest smoothing the forcing.rivers input fields more that you do now (this spreads out the effect of the river). Five smoothing passes is the minimum and you could go as high as 100 passes, but I would experiment with 10 or 20 smoothing passes. In addition you could change the relaxation to SSS at the river by either setting relax.sssrmx to 0.5 (instead of -0.5), the former skips the relaxation if climatology is 0.5 psu away from the model SSS (as it will be near a river) and the later clips the relaxation at 0.5 psu. Either use 0.5 everywhere or just near rivers.
c) The neg. dp is near the boundary, so it is probably the open boundary that is the problem. A ten grid point nesting relaxation zone is the minimum and was used for GOMb0.08 because the outer model was also 0.08 degrees. The usual rule of thumb is 5-10 grid points wide *on the outer grid*. So the relaxation zone may be too narrow.
Alan.