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upper rail setting for D3 with 16 mm/f2.8 fisheye Ser.Nr. 215894 is 68mm, 86mm on the lower rail for D3. In Portrait mode you may use 60 degree which gives you 6 stops with an overlap of 32%. PTGui calculates a HOV in portrait mode of 139.6 degrees. 6 Stops stitch very well, 1Z with +90, 1N with -90. If Zenith is tricky take 2 shots with +60 degrees pitch to keep in touch with something around you where you can more easily stitch to than to a clear blue sky. Be aware taking a zenith with +90 to shut down the camera orientation in you cameramenu, otherwise these shots will be in landscape mode. Either you turn them around in Nikon viewNX or shut down the orientation.
PTGui calculates a HOV in portrait mode of 139.6 degrees. 6 Stops stitch very well,
139.6 degrees doesn't seem very likely in portrait orientation. You would only need 4 shots around with very adequate overlap. I find PTGui estimates the HFOV to be 88 degrees, so 6 around is sensible.