So, here I am again. I guess this issue is not so interesting for lots of people here, but I am going to continue.
After my camera went into service for the second time it took Nikon Vancouver (Canada) service office 4-5 days to get back to me. Their response was that focusing is "within Nikon standards" which really aggravated and upset me as I have sample shots of the camera focusing before and after the first trip to the service center. Focusing performance of the center sensors has greatly decreased and at this point I do not see how I can use the camera with autofocus at larger apertures.
It seems that I paid $3000 for the privilege of treated like c##p by this company.
I do not expect many supporters here as it seems that most people here are not saying anything negative about Nikon. However I hope that my story will help someone to think hard when dealing with Nikon and buying expensive gear from them.
I did a test shot from about 6-7 feet using Gizto tripod with Arca-Swiss Z1 ballhead. It was leveled to make sure the camera is perpendicular to the target. I used 50mm 1.8G lens and the target barely covered sensor area (as seen in viewfinder).
Here are two shots - crops of the left top corner of the target when using central sensor.
Image before the adjustment made by Nikon service center:
Image after the adjustment made by Nikon service center:
And here is the full uncropped image (still resized to allow posting here):
I have requested my camera to be shipped back to me. I will do tests again when I receive it, but I do not expect any change now.
Also I do not know how to use the camera when shooting with large apertures. I have experienced a camera that doesn't focus properly before (my D90 and the reason I rushed to finally upgrade to the full frame D800) and it was unbelievably upsetting to see all the missed shots and chances. I am now not sure it will focus properly on subjects when I need it to. I am also not sure about the macro photography that I wanted to get into - not sure how the issue will affect the quality.
All in all I am extremely dissatisfied with Nikon and the way it handled this issue. If I wasn't invested heavily into lenses I would actually switch to Canon, even though I like the ergonomics of Nikon.
Think twice before buying from Nikon if you are not heavily invested into their products already.