I have altered the shader a bit since my last post. I now only use a single cloud texture, sample that three times and rotate each sample over the other and add the result to the sky color. I have done this as passing more was having an impact on FPS.
So I have added two new functions to the shader to do the rotation of the textures.SwirlHoriz and SwirlVert.
SwirlHoriz: This function is used to rotate the cloud texture horizontaly around the sky sphere, either clockwise or anti-clockwise.
SwirlVert: This function is used to rotate the cloud texture verticaly around the sky sphere, either up or down.
I have named this source Cloud I as I have just got a new book on HLSL and so I feel I will re work this at some point, in the mean time, here is what I have done.