just recognized that something must have gone wrong with my answer.
Looking to your pano when it is self turning I get squared blurry blocks in between which are not sharp. Are you sure you shave set lens and camera body to manual at focus? Did you tape the focus ring?
I will send you the settings later on this weekend.
With longer focal length lenses, you may not be able to accommodate the full depth of field of the scene with the lens at one focus setting. If necessary, you can shoot each row with a different focus setting. Changing the focus setting alters the fov, so you need to take account of this in the stitching. In PTGui, you can assign individual lens parameters (FOV) on the Lens Details tab. Do this for all rows other than the main horizontal row. You can use the advanced optimizer tab to optimize the rows individually or all together, as you like.