I've used Photostitch myself but have had variable results. My preference is still to do it by hand as the software packages have difficulties with parallax errors.
Here I've put the photos together by hand; each photo cropped, copied in a separate layer and then aligned. You can see the horizon problem. The joins were fixed first by slight curves adjustment on each layer and after flattening the layers by cloning. (It's not too difficult to 'fake' clouds.) I didn't adjust colour balance, curves, levels -that's personal preference.
Observations:
1) I think you had a rather dirty sensor. The spots are fairly obvious. I've not removed them.
2) The horizon was not exactly horizontal. Tripod or hand-held? If tripod, was it exactly level? I tilted each photo 1º counter-clockwise before placing. They may need more. This is a major hint in making panos in my experience.
3) There seems to have been sufficient overlap although it was not very consistent between the photos. 50% overlap gives plenty of latitude. One of them was less. This hint is important for dealing with edge distortion.
4) I suspect the time lag between shots was just a little more than click, move, click, move, click! This is the third hint - constant light / exposure.
5) I think you could have done with a darker horizon throughout the pano, for a point of reference against the clouds.
Hoping this helps. The original is still a super sunset shot.
Mr P