I think that it may be the col. width adjustments that you are making that are causing things to not align. Whenever you are adjusting the size or width of an element in the menu you may need to adjust some margins or padding to account for the new width or size you have specified. I think the best way to determine this would be to make use of the preview in the CSS Menu Writer interface and check to see what the menu and sub menus look like as you make adjustments. You may find that after you make one adjustment other parts of the menu are off until you go and update the other parts.
If you are not an expert with css this is the approach I would suggest, this is how I make use of the tools interfaces to make proper adjustments to the css.
