>I am not sure I have ever tried to focus using live view. (I hope that is what you meant)<
>The focus is so minutely and subtly out of focus, that I really have problems pinpointing anything at all as the culprit.<
The purpose of the test is to determine if normal autofocus is the culprit. If it is, then as long as the magnitude of focus error is not too great, it may be addressed with AF fine tuning, saving you the temporary loss of your D3 and permanent loss of cash. If not, well, at least you have ruled out one possible cause of the problem and, in the event that you send your D3 in for repair, you would be able to provide some help by describing the troubleshooting that you have carried out as well as the problem.
>I have a hunch I will be sending the body on for repair on Monday - this is too technical...<
See how you get on with the test first. The reason for shooting the test wide open is to minimise depth of field in order for you to more easily see where the plane of focus lies, and hence if it moves between shots.
There is nothing you can do that cannot easily be undone, and you never know: you may just sort the problem. Let us know how you get on.