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Trying to figure out a transition between the storm and the nice weather
Well, your sky is not the only issue, but I'll focus on that since that's what you seem to want help with.
Firstly, the clouds are very dark all over, even at the top. Ask yourself why this would be. Clouds generally get dark when they are shadowed by other clouds, when they are shadowed by other parts of themselves, or when they are shadowed by the Earth (AKA it's nighttime). For the tops of these clouds, none of these are the case. They're in broad daylight. They should be quite bright. I know they're storm clouds, but even storm clouds are generally bright on top unless there's something shading them. Study lots and lots of cloud photos, particularly of cumulonimbus and big storm cells. Let them get dark at the bottom, but not so much at the top. Either that, or extend more clouds over the whole scene to shade those clouds. That could be quite realistic.
You've also got this strange orange glow under the clouds. Is that from the lightning? Lightning usually has a pretty neutral color temperature. Mordor-esque volcanic activity? Make sure we see those volcanoes, and make the glow more red than orange. Just to look cool? Well...that's often a bad idea. Paint stuff with purpose. It definitely should be rather dark under those storm clouds, but I'd expect it to be a neutral, maybe even bluish darkness.
This was my first version
Well, that original version suffers more in the cloud "anatomy" department. I absolutely love clouds, and they're one of the subjects I've painted the most, but I still often feel inadequate as far as truly understanding the shapes of the clouds and the way light interacts with them and the way they interact with each other. It takes a lot of time and practice.
You might try repainting the clouds completely, first more or less copying a good reference photo, and then doing it again with a little more of your own imagination. Just don't fall into the trap of looking at a photo and thinking, Well, I don't really want reality to look THAT way, so I'll do it differently for the painting. That defeats the purpose.
I really like the idea of a storm front moving in, it just seems to me like you need more of a transition. There will be a LOT of clouds piled up on and behind the storm front, even if they're not all dark. I think it's possible to have darker/weirdly lit skies within the storm front-- orange/yellow/green skies or clouds are not uncommon when bad thunderstorms and especially tornadoes are around. But you would probably get some purplish or other colored sky "leaking" around the storm front, it wouldn't just be pure blue and then storm clouds.
My best advice is to go search for some pictures of storm fronts and thunderheads, you'll get a better idea how the clouds stack up and the sky changes.
I'm trying to fix the perspective before I render the sky. Here's my 3D model
Would the horizon still be a straight horizontal line or would it follow the green axis? I want to keep the tower as it is and fix the background instead
If you want to keep the foreground as it is, the horizon will need to be much higher. In fact, the clouds probably won't even be visible.
You can get away with perspective errors sometimes, but in this case, you've got a surface that's supposed to be parallel to the ground above the horizon line, and you can see the top of it. That never happens in real life, and it's pretty noticeable. It gives the impression that the building is falling towards us.
Changing the concept a little bit. They're will be a space vessel crashing in the forest