Wow, that's pretty cool!
It looks though as you had exposure or white balance on auto (and not fixed)?
My method of photography is pretty messy, sort of the monkey with a typewriter approach. AZ during the day can be very, very bright, which makes the shadows almost black, and in order to get (most of) the tops of the trees I had to shoot directly into the sun.
White balance was set to Daylight, Av (aperture) is set to F8.0, the camera automatically sets the shutter speed. The Arizona sky can show up a very light blue, I wanted a deep blue that the eye sees, so as the camera was tilted up I adjusted the Exposure Compensation so when shooting into the sun it was set to -2.
My secret weapon is Autostitch. The unstitched photos look like a jigsaw puzzle, some are dark and some are very light. I check the Gain Compensation check box in the lower left corner of Autostitch which automatically adjusts each photos gain so when the photos are stitched the resulting panorama does not look like a patchwork quilt.
Autostitch Options panel
