How do I fix header so that it is flush with content area?

Hello - on the site http://www.shipgt.com can you help me fix up some spacing issues?

I set everything (header, nav menu, content area) to 1000px but nothing lines up flush. We want the header, nav menu, and content area to all be aligned vertically each with a width of 1000px. No matter how many things I change, I can't see, to find the right parameter.

Also, in the content area it looks like everything (whether widgets, page text, etc.) is all a little squished to the right.

If you could please provide CSS fixes that would be awesome thank you very much for the support.

On FYI - not sure if you can help with this or not, but the plugin and wordpress installation update process from in the wp admin area breaks the site and goes to a white screen, do you know what might be causing this?? Thanks again!