In my experience - firtunately, Nikon Pro agreed - using VR with shutter speeds over 1/1000 raley has an benefit. We talked about how it was more likely the shutter will have completed its travel before VR has stabilised and thereby will blurr images, i.e. if you are using fast shutters then turn off VR. All my shots with the 400 and 600 are taken with VR off as I like to 'edge my bets' with fast shutters. When using my 7000 with the long lenses then shutter speed goes up another stop.
I can't really comment on using the long lenses on static subjects where a strong support with VR could work well with slower shutters, mirror up, etc, also perhaps offering the chance to stop down 2-3 stops on the aperture to improve depth of field.
Picking up on your shots Jim, with the 400 & x2 all my images are soft unless I stop down 1, or better still, 2 stops on the aperture. I've tried 'fine tuning', but still find I get best results stopped down. One thing I've noticed with the teleconverters and the lens wide open, one can see a thin band of very sharp grass where the camera has hit focus which may (or may not) fall in line with your subject, more so the closaer your subject to the camera. Interesting to see where the camera's focus point has hit, if it has hit - Nikon's View & Cature, plus Aperture will show focus points if you struggle to see it on the back of the camera. I guess it's obvious to say Jim, your shots are out of focus, but quite why I'm struggling to see, e.g. camera shake, missed focus... A few test shots on a tree or similar perhaps?
I do have Focal and have tried extensive fine tuning with the long range kit. I have found a ruler taped up some 100 feet away worked best for me trusting to my own judgement.
Some Red Kite pictures - not without fault, but I like 'em... There's one of teh 'White Kite' in there too.