Float both columns and then clear the floats for a more stable layout. You had a margin-left of 250px on the content to clear the sidebar but the sidebar was 251px anyway (250px + 1px border).
However Ie6 would have the three pixel jog anyway so float both columns and avoid all the issues.
You can't make your sidebar go all the way to the footer as CSS doesn;t work like that so remove all youe min-height:100% as they are no use here (see the faq on 100% height for the reasons why).
The easiest way to solve the problem is to repeat a 251px x 10px image down the content container to create the illusion of the column (faux column).
[B] background:#fff url(sidecolumn.gif) repeat-y 0 0;[/B]
border-left: 1px solid black;
border-right: 1px solid black;
[B] overflow:hidden;/* clear floats */[/B]
You should include the background colour of the sidebar and its right border in the image you make. There are ways of doing it without images but it means massaging the html and adding extra elements which should be avoided especially as the background image is such an easy solution.