I just finished all of my 200-400mm f/4 testing with the D800E.
I got the same results that I got with the D800 except higher QoF values across the board. VR made little difference at 400mm. When I put the 1.4x TC on (bringing the focal length up to 550mm), the QoF values dropped dramatically. Turing on VR brought the QoF values back up, but they were still 25% lower than shooting at 400mm with no TC.
Conclusions are the same as with the D800 and 200-400mm f/4: - Use the TC only when desperate - Always turn VR on when the TC is installed