You will need to remove the:
<!-- Header Begin -->
from the top each page to keep IE happy. You will also need to change all the width values in your menu_ie.css to 183px (same as in menu.css), and it might be worth giving the menubar div a black background so that the slight shortfall doesn't show on the right.
IE will not render some content properly if there is no DOCTYPE declaration, or if there is unrecognised input (or remarking) before the DOCTYPE,