Hi Richard, After spending some time Adjusting the AF Fine Tuning on my 200-400 on my D4, I got amazingly sharp images all the way across the full 200-400 focal lengths. Both are back at Nikon Service right now after a bad drop, but that's another story.
You mentioned going back to 0 AF. My new D800 arrived late on a Friday afternoon, so I didn't have a chance to test it. Saturday, I went out and shot a normal group of nature shots and again on Sunday. After looking at them on the computer Sunday night, I didn't feel they were as sharp as I wanted. That's when I started testing them on a LensAlign. Shots after I adjusted from +11 to +15 were much better, but I also noticed the variation between zoom ranges. At any rate, mine seems to NEED some adjusting.
I have a few friends that adjust their AF Fine Tune throughout the year based on the subjects and exepected distances. For example, with some lenses, they adjust for the long side during grizzly bear times in the spring. Then, when the songbirds start moving through and the are shooting closer, they readjust for the best results.
The takeaway of this thread might be I might need to expect more variation in sharpness at different zoom lengths than I had originally thought.