Still struggling with composition and uncooperative clouds but I gave it a whirl again with a 4:30AM wake up call and here is the first shot that I processed from this morning.
Each shot was taken at f8 2 seconds ISO 100 18mm (on a crop format camera) taken about 20 minutes before sunrise.
Since I don't have an ND filter I tried Colin's suggestion and combined four images to smooth out the water while not blowing out the sky. I added a levels adjustment to to foreground and a bit of a curve to the sky separately and then did a little bit of dodging on the really dark areas. I was really cautious about making the image too bright as I wanted to retain that sunrise feeling and lighting so the adjustments were relatively minor.
I think that I see a bit of a bump in the center of the horizon that I need to take care of but I would like to hear what you think before I go any further...