Looks like your body has back-focus problems. Not all lenses are the same, so even if the auto-focus on the body works perfectly, the variances in the lenses may make for better focus on one lens, and worse focus with another lens - all on the same body.
I have two lenses, the Nikkor 18-200 mm VR and the Sigma 150-500 mm. Both worked perfectly on my D90. When I got the D7000, suddenly I had soft focus with both lenses. I did some trials with a focus chart and even fine-tuning the auto-focus to -20 I was still getting back-focus.
I took the camera and the Nikkor lens to a Nikon repair center and they adjusted the auto-focus. I still had to fine-tune the auto-focus afterwards, but now both lenses focus very well with a -17 auto-focus fine-tune setting. Speaking to the repair tech afterwards he told me as long as one can get good auto-focus within the -20 / +20 fine-tune allowance then the camera is considered to be within specification.
I suggest you take the body with all Nikon lenses to a repair facility and have them fix it. They need the lenses as well in order to calibrate both body and lens together. You can Google and print a focus test chart if you want to run your own trials, but I feel confident from looking at your pictures that a trip to the repair center is indicated. The fact that the focus in your pictures progressively improves the more negative fine-tuning is dialled in proves it to me.