I don't see any problems with brightness in the clouds... though its a bit hard to tell at that size.
For stitching, the newer versions of PS are pretty damn good at it if you shoot it anything close to right.
File > Automate > Photomerge
and stick it on auto align, auto perspective and whatnot. Should give you a very decent start point, then you can go in to each layer and manually tweak the masking if need be.