I'm using a D3 with Nikkor 14-24 f2.8. I used in to capture my first panorama in Manchester Cathedral. I set it on manual and bracketed my exposures by varying the shutter speeds with a constant aperture of f16. I had focus on auto. Perhaps I should have set to hyperfocal distance. I did have WB set to auto and I wonder if this is responsible for some odd colour patches on some parts of the images.

Many thanks for the advice in your most helpful post and my apologies for drifting off-topic in this thread