There are a few panorama software programs out there that will use Nikon raw files to stitch together a panorama. However, to my knowledge there is no software that will save that stitched pano back to a Nikon NEF formatted file. This would be a pretty good reverse engineering trick considering how structured the NEF format is and the fact that Nikon keeps a pretty tight rein on use of their proprietary raw format.
Thanks George! Unfortunately, I am not sure I follow what you are saying. If these software applications you speak of stitch together RAW files (NEF or other), do they then require transforming said data to another format such as TIFF in order to save the pano? Why would such a file stitched together from NEF RAW files have to be reverse-engineered to be saved in the same format it started out as?
The "problem" I am having is that PS3 requires one to make lighting adjustments to any RAW file before one can "do" anything with the file. For singular images, that is not a problem. However, when stitching together a number of images for a pano, I doubt that one could repeat the stitching process a second time and come up with the EXACT same pano - especially when manually aligning images to fit. See, my intent would be to then blend these 2 resulting panos for better HDR - something that requires absolutely identical images in respect to layout. Maybe someone could suggest a workable 'work-around'?