Hi Ben,
i’m having the same problem, but your solution does not add the social icons in the navigation bar, it adds them to the top bar.
Any idea how to properly add them in the right part of the navigation bar ? I had to add the following line to includes/swift-framework/sf-content-display/sf-header.php (line 565) :
$menu_full_output .= '<li>' . do_shortcode("[social size='small' style='dark']") . "</li>\n";
… but it’s absolutely not sustainable !