I know very little about photography (and joined specifically to answer), but I do know that the wind can move particles of dust and what-have-you through the air, and at far ranges (depending on lots of other factors, I'm sure), you will see this as a blurring. From even longer ranges, you also need to realize the atmosphere itself scatters light, and therefore very far away objects can be shrouded in a blue haze with lower contrast than if you were close by on Earth.
Since some other people answered with probably better actual photography advice than myself and were saying something along the lines of your AF is dated, maybe whatever the camera body uses to detect focal point has become damaged/out of spec over the years, and it can't quite get it perfect. Coming from an electronics background, some components wear out of original specifications gradually as they age, especially any that rely on a liquid of some form (namely electrolytic capacitors).
I'm sure any sort of warping of the DSLR mirror or any misalignment of it could cause some of this, but I assume DSLRs use a glass internal mirror and therefore it shouldn't warp. Further, if the mirror was misaligned, I think it would be more blurred to one side and certainly not crisp and clear up close, however.
And finally, this might have more to do with how long the shutter is staying open (ie, vibration) in that first shot as it's quite a bit darker. I know from cellular phone camera photo attempts that a dark scene is bad news. I can't stand nearly still enough for night shots, and even sometimes a blinds-closed room is enough to get a blurred photo. I have seen that some focusing systems in cameras spin a mass internally, and if this was unbalanced, blurry shots at a distance could be an issue, as well.