You need to put a condition around the code to not show it on the index.php page:
HTML Code:
<vb:if condition="THIS_SCRIPT != 'index'">
breadcrumb code
</vb:if>
As for the stylevars for padding, I believe it's hardcoded, so just write your own to override it. Link color is just link_color, so again, just write your own if you don't want to change the link_color which will affect a lot more than just the breadcrumbs.