I've been following this thread on and off and see you are making comparisons between the D3X, D700 and D7000. I have no experience of the D3X but plenty of the D700 comparisons. Just about everyone on this forum remembers my torturous journey, from a returned faulty D7K to soft images and many issues a bit similar to yourself. I would like to offer some friendly advise to consider. Stop comparing the D7K to any other camera, let alone the D3X/700. Imagine this is your first Nikon dSLR and you are starting from scratch. I say this because of my own experiences and am offering it as I once shared a similar situation.
So, ok where am I now and what did I learn? Mostly, I listened to others and I decided, eventually, to stop making comparisons between the D700, D90, D300 etc.etc and the D7K. I started to listen to advice, but started developing my own techniques. What I did learn was over about 400mm with a speed over 1/500th handheld turn VR OFF. Use a Monopod or tripod with VR OFF on long shots. Increase the speed to as much as I could get, whilst trying to maintain between f7-f9. To achieve this I used the wonderful high ISO's if required. If you take jpegs only use the in-camera sharpening and try the different settings. I sometimes take jpeg and put mine to +7, but as I take RAW mostly and process in Lightroom 3/CS5 often the sharpening isn't an issue. The only legacy I have is that my 80-400mm does not perform well on my D7K, I don't know why, but it works fine on my D700. I now use a 70-200mm f/2.8 + x1.7TC for birding.
I have scoured my photo history. I have have now deleted nearly all the images that I used during my struggle to tame the D7K. However, I have found 2 images.
Anyway, the attached two images. Both with a 70-200mm + x1.7 TC and a focal length of 420mm (35mm format)about the same distance away, approx 150 yds and images cropped to about only 5%.approx. The first is typical of my early attempts, the second last week.
I don't know if any of this helps you or others, but persevere. Incidentally, I too went through all the tests using charts, chimney stacks comparing D700 with D7000. I got so confused my wife even said "enough"! Irrespective of what you use the camera for, landscapes, portraits, wildlife etc. my images have improved 10 fold by treating the D7K as an individual, stand alone camera with no comparisons. My technique with the D7K now bears little resemblance to that used with my D700. As with any camera some basic techniques of course remain the same.