Oobah

You seem to put it a bit too complicate; all that is really needed is a few shaders, that automatically change the effect on the skybox. Lighting, though, is a different matter... you can't easily set up a day and night global lighting, unless you resort to that Rend2 effect that simulates the day and night lighting.

I'm not sure how to do it hence why I'm curious. But hey someone wants to make a tutorial for it I'm all for reading up on it!

From what I can see, there's at least one simple scrolling shader for the moon (which, additionally, has another shader for moon phases maybe? I digress), other scrolling shaders for the clouds, plus effect-generated clouds. As for the sky, I believe he used a starlit skybox, and around that, a set of shaders that 1) slowly fade in and out the blue day sky, and 2) slowly fade in and out the pinky colorations of dawn and evening. Plus the Sun, I guess, another scrolling shader.