Hi Dom, I think what you were trying to achieve with your first incarnation of this scene is worth pursuing. To me, the clouds were never the issue, in this and the previous. What I am concerned about now is what you want people to look at.
It's not a bad idea opening up your scene to full sunlight, for two reasons. One it allows you to get colours / displacements right, that when two, you roll back to your preferred lighting, you have every confidence in your scene so that all your efforts are then focussed on getting the mood right.
The tree model you've used is strong enough to be the 'hero' focus. In fact, I'd be tempted to go back to your old scene, position your camera in a spot where you can use the god rays to backlight a silhouette of Walli's model. Have a read up on the Golden Ratio. Think about where you want a viewer's eye to go first, concentrate on that, and then work on the periphery afterwards to add depth to your composition. Also use the copy coordinates feature in your preview window to position individual models exactly, it doesn't matter if things should be correct, it's more important to get people to believe in your composition.