I spent some time making changes to the clearfix.css. When I made changes to the main menu order all of the CSS changes back to the default. widgets, H3, header text all of it.
When I revert to the original menu order my CSS shows up. When I change the menu order and paste my css back in the website remains in the default state.

Can you be a little more detailed like a step by step flow of what you are doing and where you are doing it.

http://39b.5b2.myftpupload.com/
Resize the window and you will see it.

Here is what I would do
1) export your settings (MTO->Export/Import)
2) go to each CSS file and
- one at a time reset the CSS for that one file and
- test the front end till you fine the batch of CSS causing the issue
3) Import your saved settings from step 1
4) Copy all the CSS from the group causing the issue to a text file
5) reset that CSS group and copy all the default CSS to another text file
6) compare the two files and note the differences
that should give you a handle on what is causing the issue. You might have to take out and test each change to narrow it down even further.

Let us know what CSS was causing the issue.

What is it that you are trying to accomplish? Do you want your menu to stretch out across the header, under the image, or do you want it to the right of the image? There's not enough room for the entire menu to the right of the image, since you have so many menu items, and there's no way to prevent the menu items from folding to a second line.

If you want all of your menu items to stretch all the way across, you should take the nav element from out of the banner DIV and create a new DIV on the same level as the banner DIV, with a class of row. Then change the class of the nav element from col7 to col12 (and the class of the logo-area DIV from col5 to col12).