Focus Stack Retouching

Ian, while you very briefly touched on the fact that you can use any of the images from the stack you used the first one which is the closest focused image. For the clouds most likely the last image of the group was the one that was truly focused on the clouds. I personally would have selected the last image to correct the clouds, starting with a larger brush to correct the areas with only sky & clouds and no other close objects such as the branches of the dead tree. Then I would have reduced the size of the brush to a much smaller size, , increased the brush hardness and zoomed in some and brushed around the branches to correct the clouds near the branches. I have used this technique extensively and while a bit time consuming yields very good results. It is also useful with you have motion of trees etc. due to wind. Helcon will sometimes get confused about which focal distance to use. Using a small brush size, I will select the image that has the best focus for the object and brush over the areas Helcon wasn’t able to properly identify.

I know this was just a demonstration but you also briefly brushed over the mountain which would have caused it to appear out of focus.