This is one way to deal with tripod shadows.

Here is the first picture in the sequence.

There is a very bad shadow at the bottom of the picture.


You can see another set of lighter shadows to the right of the main shadow.  All need to be removed.

The objective is to move your rig around taking additional shadow free pictures.  This will give you material to use in order to remove the shadows.

I offset the tripod to the left and rigth taking additional pictures.  You can see that the center area is shadow free. 



After blending the three pictures, here is the shadow free version:


The Nadir shot also requires attention.

Again, I took a couple of pictures after moving my rig over both directions.



After blending in Photoshop I have a shadow free Nadir shot:


Since I could see that there were several light sources in this panorama I knew shadow control was going to be an issue.  I used a monopod mounted on a mini tripod in order to minimize shadows.

The objective is to take as many additional photos as needed in order to have enough material to use to remove your shadows.

Here is the resulting shadow free panorama (click on image to load panorama):