Hi,
Please begin by adding this to your theme custom CSS:
.page-header-naked-dark .header-left .aux-item,
.page-header-naked-dark .header-right .aux-item {
border-color: transparent;
}
.page-header-naked-dark nav .menu ul.sub-menu,
.page-header-naked-dark li.menu-item.sf-mega-menu > ul.sub-menu > div {
background-color: white;
}
.page-header-naked-dark a.sf-button.standard.sf-icon-reveal.checkout-button {
color: #ffffff;
}
That should sort your header lines and cart dropdown color where the naked header exists.
-David.