>>I don't think it's too unusual for SLR cameras to be off by a tiny bit, as the film plane and the focusing screen are always going to be off by a tiny bit, which will of course only get worse with age.<<
On digital cameras? My FTN and F2SB still focus the same way they did 30+ years ago.
If you're going to focus a MF, you should see if there is a focusing screen with optical focusing aids available for it. I thought Nikon made one for the D3S, but apparently not. KatzEye only lists one for the D700. If you think you'd like to have the option to focus optically, give KatzEye a call and see if there's something they may be able to do.