"Based on your data, your two D800E bodies seemed to have a similar AF Fine Tune difference for most lenses. Am I understanding you that the difference is attributed to the body? And if you wanted, could be adjusted in one of the other bodies?"
It appeared that each body had a built in offset for the AF fine tuning. The D800 was a little more positive than the center D800e in the table. The right D800e had a 4 to 6 point lower offset from the D800. To me, this shows that each camera body has a built-in bias for AF fine tuning. I have seen from my own experience that this offset can change. I damaged a lens last year in a fall. After I had the lens repaired, I found that I had to rerun my AF fine tuning between the camera body and the repaired lens. I also had to rerun the AF fine tuing with that same body and all of my other lens. The camera was not damaged in the fall, but the AF fine tuning bias changed.
"It also looks like the teleconverter creates some issues. The AF Fine Tuning was maxed out with the 70-200 and teleconverter. That seems to indicate a problem mating the two or some other issue."
Because the AF fine tuning with the TC installed maxed out for all three bodies and did not follow the typical AF bias pattern for a body, I would say that it is a good candidate for a Nikon repair. To my knowledge, it has never been damaged and is only two years old. However, the data shows that it is a problem.
"Were the quality of focus measurements similar as well? I was thinking that its possible that one body is simply sharper - and because it can resolve more detail, it might require more adjustment but still be sharper at all measures."
I found the quality of focus (QoF) to be about the same for both D800e bodies for each lens. However, the D800 QoF was significantly lower for each lens. When I questioned the FoCal folks about the difference, I was told that the QoF values are a relative measure for calibration only and should not be used as an absolute measure of the difference in capability between bodies. They also said that they hoped to be able to show the difference in sharpness between camera bodies in a future release...maybe version 2.0 and beyond. That was last fall. I have not questioned them about that capability again this year. By the way, I did sell the D800 after doing all of the lens tests. I knew I would not use it because I would always favor the D800e body that had extensive data showing it was sharper.