"But since getting the camera back, I cannot help but wonder if there was a slight miscalibration of the AF system."
Before or after
The bird shot looks pretty good to me especially at 1/200 and a focal length of 300mm through those branches. It may be hard to tell if performance is any better because your D7k was working pretty well for you from an AF standpoint anyway.
I know what you mean about the VR and overall quality of images from the kit lens. I work at a school where we have a photography course for adults at night and so many will ask if there really is a difference between a consumer lens and a pro lens (same thoughts I once had) or are they just more expensive. It is a kit lens and while certainly a very reasonable lens that is what it is. I bought mine used simply because I wanted a decent walking around lens with a decent zoom range that i could use for snapshots at family gatherings, parties, etc. I always have to remind myself of that when i start to look at the results a little too closely (pixel peeping), although when I do decided to look that closely when there is a lack of focus issue it is 99.9% my error and not really the glass.
It sounds like you can now enjoy the camera for what it is rather than dealing with the oil problem so go and enjoy it.
Marc There are always two people in every picture: the photographer and the viewer.-Ansel Adams