Drop a new sky in and change the layer's
blend mode to either Darken or Multiply.
I choose Multiply for this image.
Apply a layer mask and tweak to your liking.
Curves Adjustment Layer to increase luminosity (because
the Multiply mode makes things pretty dark).
Paint With Light.
Flatten.
Dupe Background and apply an Orange color Photo Filter
(Image>Adjustments>Photo Filter) to match the color of
the vegetation better with the clouds. Masked off the clouds
which were that color to begin with.