Just to clarify V-Spec did you find both MKIIIs to be highly reactive with their focus? I've heard of lots of problems with the 1DsMKIII and AI Servo focus issues but I am interested to hear from someone who has tried them all together.
Both MkIIIs have identical focus, its the quickest of any camera to attain actual first focus, infact its totally instant from the moment you pump the shutter. The problems are with a constantly moving subject like an athlete running towards you, where both cameras will produce a few oof frames because they over estimate the forward movement, which leads to front focussing. The D3 has a delay before obtaining first focus, which makes things more difficult for fast action stuff, on the flipside it doesn't "hunt" when it fails to focus.
The Canon can sometimes get lost with big glass if it "misses" and focuses to the background with a small subject - the D3 doesn't do this but on the flipside it takes a lot longer to actually focus, which is why it sucked with the Puffins in flight and at Bempton when I used it both times, with a 300 and 800mm lens.
For me the files off the D3 are brilliant straight off the camera, but when you use either Canon below ISO200 it surpasses the D3. The colours are nice and smooth and there is more detail present. When you take things above ISO 800, the D3 pulls away.
The 1DS MkIII is worst for noise, as there are so many pixels, ISO 400 isn't that great, the MkIII is far better for noise - that said no camera resolves as much detail as the 1DS MKIII. If your good at processing and can deal with the noise, you end up with bigger better pictures. And with the 1DS MkIII you can still crop significantly and be within agency guidlines for image size.
They're all good cameras, but some do other things better, its retarded to say that "The D3 is a better camera overall" because it blatantly isn't. I can't shoot birds in flight, or ultra fast action stuff with the D3, however I can't shoot at ISO 6400 very well with the MkIII, they both do different things better than each other... Whichever camera you need depends on what you mainly photograph..