A background-color …. mmm, maybe something that rhymes with the logo line-style like a border would be a better fit:
.menu li a {
transition: all 0.3s ease;
display: inline-block;
color: #444444;
font-weight: 400;
font-size: 1em;
padding: 15px 0;
border-top: 4px solid transparent;
text-decoration: none;
}
.menu li a:hover {
color: #964800;
border-top: 5px solid #cf7019;
}
Or reuse that striped separator:
.menu li a {
background: url(img/separator.png) center 50px repeat-x;
}
.menu li a:hover {
background-position: center bottom;
}