with your settings, the z-fighting in the clouds is gone, but when terrain and clouds are intersecting there are still some problems.
http://img28.imageshack.us/img28/6195/cloudsfighting1.png
The depthbuffer description is following:
dsDesc.DepthEnable = true; dsDesc.DepthWriteMask = D3D11_DEPTH_WRITE_MASK_ALL; // or D3D11_DEPTH_WRITE_MASK_ZERO dsDesc.DepthFunc = D3D11_COMPARISON_LESS; dsDesc.StencilEnable = true; dsDesc.StencilReadMask = 0xFF; dsDesc.StencilWriteMask = 0xFF; dsDesc.FrontFace.StencilFailOp = D3D11_STENCIL_OP_KEEP; dsDesc.FrontFace.StencilDepthFailOp = D3D11_STENCIL_OP_INCR; dsDesc.FrontFace.StencilPassOp = D3D11_STENCIL_OP_KEEP; dsDesc.FrontFace.StencilFunc = D3D11_COMPARISON_ALWAYS; dsDesc.BackFace.StencilFailOp = D3D11_STENCIL_OP_KEEP; dsDesc.BackFace.StencilDepthFailOp = D3D11_STENCIL_OP_DECR; dsDesc.BackFace.StencilPassOp = D3D11_STENCIL_OP_KEEP; dsDesc.BackFace.StencilFunc = D3D11_COMPARISON_ALWAYS;
Maybe i missed something?

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