HDR postprocessing

I took a look at your raw files and identified couple of problems.

Firstly, lots of parallax which leads to suboptimal stitching result. There will be visible seams in the final panorama. The images were probably taken hand-held?
Secondly, veiling flare in the second topmost image. Some kind of protective filter?

Using auto exposure to cover the dynamic range of the scene was a good choice in this case. Single, well-exposed image covers the brightest part of the panorama and the darkest parts can simply be brightened to match. There will be some additional noise, but that’s not much of a problem.

Anyhow, I converted the NEF files using Raw Therapee, using very neutral profile (only white balance was altered) and stitched the images in Hugin without many problems. The exposure differences between the images were leveled and this was the result: https://dl.dropboxusercontent.com/u/168254285/web/hugin-nd750_a4076-a4079.jpg

The panorama was then opened in RT and auto exposure, tonemapping and couple smaller adjustments were enabled, and here is the result of that: https://dl.dropboxusercontent.com/u/168254285/web/nd750_a4076-nd750_a4079-rt.jpg

you obtained the second image by editing the first jpeg? why did you not export it as a tiff? that would have clearly given you better resolved brightness steps to play with.

Also, your result looks quite nice given how little processing you say was involved. So what was the difference?processing in RT before stitching? How can a white balance adjustment before stitching have such a great effect - clearly you could recover more color from the sky than anybody could based on my TIFF.

I didn’t touch your TIFF. I stitched this the ground-up from the provided NEF files. The re-stitch is what makes the difference here as all the dynamic range in the source files is retained - sky is not clipped to pure white.

So why was the sky clipped in my stitch but not yours?

I set the exposure value in Hugin so that nothing would be clipped. Dark image can always be brightened, pure white (clipped) can never be recovered.