Hi
I just cropped the photo to move the tree to the left and remove the top layer of clouds, I then used the clone tool in Photoshop to work over the branches of the tree that were going out of frame and replace them with blue sky, its not very well done as it was a quick edit on the small size file, but given some time and the large file you could do a great job with it and really finish off the image for a nice effect.
Thanks for letting me know all that you did in the edit. Thanks too for taking the time to help a newbie out. 
At least you are in an area where there is a multitude of things to photograph,
