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I like the concept and every change you propose. The layout is elegant and clear and it's heartening to see you have discarded the separator squiggle which looks straggly and out of place. The new contrast of shades between columns is a more mature separator.
This is a drupal site, isn't it? I think it's a fine example of what a marvellous and flexible CMS drupal is.
However, there is one weakness which has existed from the beginning and is still there in this new design: the header. It is astonishingly bad. I wince each time I look at it. The contrast with the body is violent and disturbing. There are many sites which use this sort of header, it is a current fashion and sometimes it works well. But here I'm afraid it fails. It gives the whole page a disconcerting, ominous, louring, poisonous and sickly crisis. Aggravating it is the crush of detail contained in it. Far too cramped - it reminds me of the experience of the last gasping fish in a world whose oceans have all but evaporated. This is the only site on my daily viewing list that makes me anxious - and only because of that header. If I had Roman Abromovich's billions, I would bribe you a luxury yacht to change it. As I am all I can do is exhort you in the spirit of bonhomie and gratitude for an otherwise super site to rid it of this horror.

I like your passion about the header - we'll take it into consideration. :)
It's not a drupal site. It's a custom application on a .NET framework.