Just an update.. I checked out MenuAdapter.cs out of curiosity and ran across this:
// Menu.css
Helpers.RegisterEmbeddedCSS("CSSFriendly.CSS.Menu.css", type, this.Page);
It looks like that's some sort of funky way of representing a directory structure. Normally, it would be CSSFriendly/CSS/Menu.css. That's what I assume, anyway, so if you drop your CSS file into the CSS folder and change this line to:
// Menu.css
Helpers.RegisterEmbeddedCSS("CSSFriendly.CSS.YourStyleSheet.css", type, this.Page); then it will reference your stylesheet. Instead of going through the rest of the code behind file and changing every reference it makes to their CSS classes, I recommend just copying Menu.css into your stylesheet and adding/changing whatever you need. To get it to recompile the DLL, just create an App_Code folder under the root directory of your web app and drop the new MenuAdapter.cs in there.
Hope it works! :)