Thanks Steve. Your response contained a lot of information already known to me, but I appreciate your thoroughness. The factual content will be useful to many other readers of this thread.
All I can say is, I must be extremely lucky or you have a much keener eye for focus issues than me
I have tested each of my Pro lenses after purchase for front and back focus and found them all to be excellent. I also often shoot small birds with my 300mm f2.8 VR at distances of around 6 feet, and never noticed a focus issue. I also use this lens with the new 2x converter, as it allows me to shoot a lot closer than a 600mm lens, and not noticed an issue.
My 105mm Macro was perfect and so was my 70-200 f2.8 VRII, straight out of the box
I totally understand your point about tolerances, but my experience has been that these tolerances are tight enough with Nikon's top end equipment, as to not be an issue. Well, I haven't found it to be an issue... Yet! Obviously your experience has been different, and I will now test my lenses, if I get any inclination that they have deteriorated.
I once had a Sigma 150-500, and got so frustrated with it, due to the fact that I could never manage to fine tune the focus to my satisfaction, that I sold it. That was even after Sigma had had it back for calibration! So as you can see, I am fussy.
I read a fantastic article on focusing tolerances once. I wish I could remember where it was, so as to link to it. Sorry Steve.