I applied a mask to the sky layer to paint in the areas I wanted to erase. It's a good idea to keep these edits non-destructive because you never know when you're going to need to come back and change something later. The mask can be seen in Fig.06, where the white parts were meant to show and the black parts were blocked off. I was able to paint into the sky fairly easy with this.
I started to roughly paint in some buildings that stood out (Fig.07). Adding highlights to the left side of the city made the image more balanced. With the right side dimmed down, the differences in the original photos weren't very visible anymore (Fig.08).
I used the Polygon Selection tool to create some shapes for the high-rise sci-fi structures (Fig.09). With that selection, I was able to paint gradients inside the shape and maintain a sharp and crisp edge. I used this technique to make the base for the center structures.
Some structures were added with custom brushes. These little doodads can add a bit of interest to the image and make the silhouette read a bit better (Fig.10). I want to point out that the fog is heavier at the bottom to make the bottom of the structure lighter and closer to the tones of the city. This gives me a good and gradual change to the tip of the structures where the silhouette is dark against bright, and clearly readable.