Let's not let the "scratch" detract from the real issue here. You spent $3000 of hard earned money to buy a product that does not work properly. It was sent in for repair at your cost and it came back worse than ever.
Several years ago I had a similar problem with a D700. It reached the point where the second repair resulted in a camera that did not function at all. I contacted corporate Customer Service and would not let up until they sent me a brand new camera that worked. You may want to try the same approach.
Nikon has not handled the left focus issue very well. I'm really disappointed in them. Trying to get a camera repaired by them seems more of a crapshoot than good old fashioned reliable service.
I hope you get your problem solved promptly one way or another. You deserve a much better experience than this.