I know this is a little late. Your website is quite unique. However the homepage confuses me. Maybe it's because of the industry you're in that I'm not used to the layout of it.
A couple things you could do is put actual content behind the links in the footer area, or take those out. It's easy to do in the footer php file. Ocassionally check your links for functionality. The 'US Patent and Trademark Office' link doesn't work properly. I'm also not a fan of pages running long in the sidebar area but short on content (your Branding page). But that's my opinion. If you really need that layout, then so be it.
I DO like that you have a second header/banner in the area below the footer. When on a long page, it wouldn't be as easy for a user to forget which site they're on. And I also like how you have some pages set up with your sidebar in different places. For some users, it may be more confusing, but for savvy people it's refreshing.
How is the site working for you? Has it increased business?