Everything on the page has been designed to fit into a 1001px width. Since you changed that it had to move some things down since they will no longer fit within that area. You will need to change the placement of some of the items to fit in this new width. The search box will have to go somewhere else. It will not fit next to the menu at that width. The width of the search box is 300px and you are reducing the width of the page by 220 px, so this will not fit where it is currently at. You may want to try moving it up in the page, or maybe in the left column. Just a suggestion.
Also the featured items box will need to be made smaller to fit into that width also.
