I've done some panos before and was quite happy with the results but I do have a couple of questions/comments about yours:
1. Why didn't you shoot at f9 or f11? Maybe your lens has the "sweet" spot at f5.6 but with a higher aperture you get more DOF which in this particular case would have been fine. Of course I can't see the details at the resolution you posted but if you are going to downsize it to 3000 pixels on the long side even the f11 would look crisp sharp (even if it's not the sweet spot and to capture more detail in the trees).
I assume 5.6 is the sweet spot as it is highlighted in another colour on the lens & that is why I used it. I get your point but must say all was in focus with the focus at infinity.
2. I never ran into a stitching/overlay problem using the regular mount plate for my tripod. I like your rig but I think in your case it's overkill. Your subjects are so far away that it doesn't matter if your panning perfectly on the axis of the pivot point.
In my experience it would only be necessary to use your set-up if you are making a pano of something where you have subjects also very close to the camera. There you have to have a pan exactly on the pivot point to prevent alignment issues.
Good point.
3. If you set the lens to f5.6 so that the camera had no control over aperture and your exposure time, ISO and WB were manual and never changed it's likely that the stichting software screwed up making the images brighter/darker. I'm using PTGui for panoramas and love the software. I get very little brightness issues.
This lens is manual aperture & focus on a 2x crop body; the ISO was set to 200 & WB to cloudy. The frames were shot in raw & all but the dark frame were processed exactly the same in Lightroom 2. I could understand the dark frame seams showing if I did not get a good match with the others so possibly as you say the problem comes from the stitching software.
4. I think a second row of shots showing the tree tops and more sky would have made the panorama perfect. Just a personal thing. But otherwise it looks good.
Not sure I understand this comment, there is only a single row of six shots.