It's a very nice shot. Of the three versions you have posted, I prefer the natural one.
I have a somewhat different approach to this sort of thing. My goal is to reproduce what I perceived when I was there.
Your third version was an improvement in some ways, but the excessively blue shadows at left centre and the loss of definition in the clouds were not good.
I've reworked the natural version using a combination of Camera RAW and Photoshop tools.
I started by adding a bit of clarity, vibrance and saturation to the whole image. Then I worked on local adjustments using the dodge and burn tools in Photoshop. I selectively burned in shadows to enhance the texture and solidity of the rock faces, and to make textures more consistent across the image. In the sky I burned in midtones to darken the blue sky, then dodged highlights to lighten the clouds. I then used hue/saturation in Photoshop to tone down the sky blue a bit, as burning in the midtones had made the blue saturation a bit excessive. The goal was to make the sky more interesting.
I could be tempted to lighten the heavy shadow in the lower right, but would want to have a higher bit depth file for that one.
Most or perhaps all of these adjustments could be made in Lightroom using the Adjustment Brush thingie, but I'm more comfortable in Photoshop.
Hope you find this useful.