Thanks for clarifying the steps that you used. 
The problem of curved, or even undulating horizons, as well as distortion of areas near the camera is very well-known to people doing panoramas. As I suggested in my previous post, it's almost always caused by a camera that is not level and/or not rotated (between exposures) around a perfectly vertical axis. In fact, people serious about panoramas actually use spirit-level type devices to level the vertical axis of their tripod together with artificial horizon tools on their cameras to level the mounting of the camera to the tripod.
Probably the best way for you to become acquainted with this aspect of making panoramas is to read some of the excellent articles on the subject. These are much more comprehensive than I could do in this thread, e.g.:
http://www.theperfectpanorama.com/articles/problem-6-horizons.html
or just Google {panorama stitching curved horizon}
At the next level of care in generating panoramas, if you don't rotate the camera around a very specific point in the middle of your lens, then serious problems in the foreground develop. Of course, entrepreneurs have come up with specialized equipment to attach a camera to a tripod to allow rotation around the nodal point. For example, look at these devices (in order of increasing price, the last one being automated):
http://www.bhphotovideo.com/c/product/838676-REG/Nodal_Ninja_N4_PKG_NN3_MKII_Starter_Package.html
http://www.bhphotovideo.com/c/product/889880-REG/Manfrotto_mh057a4_long_Deluxe_Panoramic_Head_Geared.html
http://www.bhphotovideo.com/bnh/controller/home?O=&sku=689697&Q=&is=REG&A=details
Of course, many people want to take panos without going through the preparation steps described above, so better panorama stitching software includes tools to try to help them out. Of course, the results are never as good as if you "got it right" in the camera, but are a very useful adjunct if you got it close in the camera and just need the software to make some small tweaks. These tools are much easier to use than do-it-yourself approaches such as the one using the Adaptive Wide Angle filter that you tried. Here are some links to such software:
http://www.ptgui.com/man/straighten.html
http://www.johnhpanos.com/horizons.htm
HTH,
Tom M
PS - If I had to pick just a few hints to give w.r.t. making hand-held panos of landscapes with lots of interesting things above and below the horizon, it would be to:
(a) turn your camera to the portrait orientation (instead of landscape) so you can take just one row of shots, not two or three rows;
(b) allow plenty of overlap between the component images;
(c) do the absolute best you can to keep the horizon in the center of the viewfinder; and,
(d) don't just turn your body to take the component shots, but rather, shuffle in a tight circle around an imaginary point located in the middle of your lens.
(e) don't immediately crank your lens to it's widest angle position. Instead, use a normal or even a telephoto focal length, but take more component shots.
(f) try not to include too much foreground.
To prove that one can get reasonably good results with spur-of-the-moment hand-held shots, I made the attached image by following, as I recall, all of the hints given above.
