Unable to do a clean install

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I need to reorganize the header because the logo is a long one rather than a square one. And the TOP MENU items are numerous. I would like to slide the top menus under the logo, please reference attached screenshot. When I try to change the #topmenu_pad width the top menus slide under the logo but the last menu item, 'References & Links' still wraps under. Changing #logo width and height does not help either. I need some expert guidance on how I can make this fix and which css file I need to edit.

Also, on the bottom left the breadcrumb links appear even though I have turned them off. Why do they still appear?

Thank you.

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