I just ran a new series of tests today on another D800E. I printed a new target using an inkjet printer for the AF fine tuning and aperture sharpness tests. I found that the new target made no difference in test results (my old target was printed with a laser printer).
However, I did find that proximity to target made a big difference when running the 51-point multi point sensor test. If I use a single sheet of the multi point target and move the camera close enough to fill the screen with my 24-70 set on 70mm, I get much lower QoF numbers than I get if I move back to 3.4m and move the zoom to 50mm and use nine of the multi point targets tacked edge to edge on the wall (3x3 grid). The ratio test showed higher quality focus across the board...and more even results for the sensors. The sensors with the lowest quality focus were still the lowest...just not as much lower as they were close up.
Are all of you folks using a single sheet target for the multi point sensor test?
By the way, the 200-400mm with the TC on still showed much lower QoF values than when it was off (35% lower). I also ran that test at 400 ISO to get the shutter speed up; I also turned on VR. With VR turned off, the shutter speeds were too low to do the AF fine tuning (vibration from my hands touching the camera to change the AF settings...or Brownian motion maybe...who knows...cause I pausded after every AF change before hitting OK for the test to run).