Thanks for the little mockup.
To answer some of your concerns:
Losing the clouds: I think the clouds are an important, but subtle way of reinforcing the idea of "The sky's the limit", since my logo is a hot air balloon. Losing these would mean losing the tagline.
The 3 header backgrounds: The background of the three headers could be improved upon, I suppose, but I wanted to make them come alive a bit more than just using a flat background.
The font: The font is something that I really like and I think it works well, especially for the individual portfolio pages. Changing it to the font for my logo would be wrong because you should never repeat the same typeface used in a logo on another element. It should always support it. Ironically, I'm considering changing the logo typeface to something else because the kerning on that particular font is terrible. If I had a copy of Gotham, I'd definitely be using that instead.
Cheers for the feedback!