Changing Font sizes for Top & Secondary Menus and the Slogan on Home page

You can override current fontfolio css style rules with your own.
I added "custom-styles" folder inside fontfolio/styles. (only on latest version 7.x-2.7)
In that folder you will find file named "my-custom-ff.css.txt".
Rename it by removing ".txt" extension so now its name will be "my-custom-ff.css".

How do I go about adjusting the size of the font used for the slogan and the secondary menu and top navigation menu?

To override existing styles you can start with assigning new font size to:

#site-slogan {
    /* change what currently is: */
    font-size: 20px;
}

/* You can also assign font-size to */
#header_menu {  }
#header_top a {  }

Hope it helps