Took a stab at it, mostly multiply masking, sharpening and a trim to rebalance.
The expanse of the sky pulls me up away from the town. Diggin' the layering of the cloud banks, and that uppermost cloud bank pulls me there as it could be an interesting subject itself. It is quite nice. It is a lovely capture and I rather prefer your clouds to mine, but mine are mostly an (unrefined) illustration @ how the change pushes things around a bit..
How you approach it will likely depend on whether your focal (what's the) point you want to draw your viewer to is the sky or the town. Either can work, I think it just needs a bit more of a "push" one direction or the other as it seems as though it wants to be a picture of the town, yet I keep drifting to the sky. Right now, I'm torn between sky vs. town. Several ways to go, so this is just but one direction.
I like your overall processing of the image and wouldn't go too dark on the clouds. The first image is lacking punch in the buildings. The re-work you posted is preferred. Crop to suit your vision and you've got a very nice photo.
