I have made some progress in the Muir Grove Cathedral panorama. I went
back and shot it over using HDR, taking about 450 shots in 9shot
bracketed, 1 f stop sets. When I got back and stitched them together I
still had the strange artifacts in the forest floor because of the
changing shadows over the time it takes to shoot all those images.
I tried various strategies to get a good final output and the best
technique turned out to be blending the bottom, middle and top of the
full image in three separate strips and then using PTGui in non-HDR mode
to combine them and output the final equirectangular image as a layered
.psb file. I had to do a bit of manual work in Photoshop to get rid of
the shadow inconsistency artifacts and then the image worked great.