>I also noticed something else regarding the alignment of the >sensors ........The center focus point using Live View does >not match the center focus point through the viewfinder
There essentially is no focus point with live view as with viewfinder AF.
With the viewfinder there is a separate focus sensor for the phase detection AF. Being that the light from the lens is deflected by a mirror through a beam splitter onto a sensor, there is multiple failure points that need to be aligned. With live view the contrast of the image from the actual sensor is analyzed. As such live view will always be more accurate than viewfinder AF. And depending on the person, manual focus might be better than live view AF.
Phase Detection AF is tolerably accurate but rather fast. Live View is a bit more accurate, but considerably slower than Phase Detection. A good article define the issues with AF can be found here at LensRentals. You might notice that in their testing there really wasn't a huge difference between LV and ViewFinder AF.
An issue I see with the focus chart tests you did, besides alignment, is that they seem to not be illuminated very well. Phase Detection AF is dependent upon good light. The better the illumination the faster and more accurate it will be I believe.
If you are going to set a up test, you should do your best to eliminate as many variables as possible. About a year and a half ago I was testing my D7000 for focus. I posted this test image in a thread I started. It's a 100% crop I believe.
As you can see by the texture of the paper, the focus was just about dead on using a Nikkor 17-55 f/2.8 wide open at 55mm.
I determined that out of my 6 lenses, only 2 needed AF Fine Tuning to get acceptable focus.