I agree that Nikon needs to take care of their warranty responsibilities, and certainly should not make a camera worse when servicing it.
The best approach when getting any new product is to use it and if defective, return it to the seller for a replacement or repair. Failing that, you need to deal with it through the warranty process.
The OP, by his own admission, bought the camera then let it sit around for a few months with out any or much use and no real analysis of it's condition. Seems odd, give all of the uproar over this issue. Many others, got a D800, deemed it defective, and held on to it because it was in short supply in spite of the known defect in their camera. Again, they elected to make fixing the problem more complicated for themselves. Many of us got perfectly good cameras out of the box, I suspect far more than received ones with problems.
Regardless, Nikon does need to fix these cameras under warranty. If their service center is failing, they need to be held to account. And the OP needs to get a fully functioning camera in the end. But he did make his life more difficult by waiting to address the issue until after the normal return period.
If he feels strongly enough about this and feels he is not getting satisfaction, he should pursue remedies afforded by consumer protection laws in his jurisdiction or hire a lawyer. Given his level of dissatisfaction, he should likely switch camera brands. No sense being a masochist.