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And it was using a featureless cloud to focus on. Good luck with that. I am pretty sure now that the AF sent your lens past infinity. This makes everything look ok, but not critically sharp on my lenses.
By the way, this is far from hyperfocal. If you want to use the DOF master to find DOF here, change the focus value to 10000 feet or so. That's as good as infinity. Your cloud was probably at least a mile, so you could use that value.
But in truth, your AF probably failed here because it had no contrast to work with.
I took your CR2 and worked with it. Thats a lot of noise for an iso200 shot. I did some Topaz NR and when I finished ran a Topaz Pop action. This action brings out the noise at 100% so I probably needed to take a different approach.
I cleaned up some of the dust, time to send it in. Never try a wet clean on this camera. I did when I fist got it and Canon charged my insurance $2300 for a new sensor when I broke the top sensor filter.