Actually at a closer look, it looks like the image brightness is varying from image to image a bit too. If PS can't handle it, try throwing them in autostitch and see how it comes out - it seems to handle brightness/exposure variations a bit better.
I'm not sure if you adjusted the exposure between captures (its a good idea not to for mosaics - but you probably know that!
) or if transparency varied (high thin cloud maybe???
).
Great first effort though!
Al.