Hello,
A few answers to many questions, maybe you can find more in the documentation.
PRANDTL NUMBER is the keyword for the Prandtl number, the default is 1., you can also change it in subroutine CSTKEP.F where you will find a number of others parameters.
With thermal effects and stratifications we favour the k-epsilon model, but too much vertical mixing may not be linked to this model, but rather to the numerical diffusion of advection schemes, and also to the movement of planes in the mesh, which triggers advection in the transformed mesh. You can try to have fixed planes.
The various diffusion coefficients like COEFFICIENT FOR HORIZONTAL/VERTICAL DIFFUSION OF TRACERS are the molecular viscosity if you use k-epsilon (they will be added to the turbulent viscosity).
With best regards,
Jean-Michel Hervouet