Johan,
I'm not sure the D100 is supported for the Nodal Ninja 3 (with the 90 degree tilt up) Regardless you don't need the up shot 90+ % of the time. Simply cube the image and clone & heal the zenith area. The patch is quite small.
Looking at your examples (stitching wise) you have got it pretty much perfect. You must remember that the Nodal Ninja 3 in not a precision panohead and removing and replacing the camera will knock things out ever so slightly. But this is no big deal really. Tilting the camera up 5 to 10 degrees with help you close the zenith hole.
The stitching parameters DO influence the stitch and this is something you need to play with in Panoweaver. Test and test again until you find the best settings for your camera/lens set up.
I personally don't thing your main issue now is improving the stitch as it is very good. You should be concentrating on your shooting technique and using your camera to it's optimum. Your images are different colours in these examples. This is a clear indicator that you haven't set your white balance and got your exposures correct across the panorama series of photographs.
Keep at it, your doing well.
Regards, Smooth ![](smileys/smiley16.gif)
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