Let me share my FF & IE "learned the hard way"
Lesson 1, FF is forgiving and IE is not, if you are missing a closed tag FF will many times still deliver the page, IE won't and everything appears bonkers.
Lesson 2, FF and IE won't space the same so you have to watch those exactly placed items. Test in both browsers often as you are coding, it truly blows to finish a page just to realize that your perfectly aligned menu in FF is sitting in your banner in IE. Sometimes you have to find the happy medium.
I didn't look real hard at your code but you have a lot of tags, go through and match them all up would be my first check. Padding is the content inside the box/container. margin-bottom:15px; Will serve you better