You should be posting in the Atheme Template Support Thread for this, so the maker will be more likely to see your questions.
To correctly remove the "Home" link, delete this:
PHP Code:
<li><?php echo '<a href="' . HTTP_SERVER . DIR_WS_CATALOG . '">'; ?><?php echo HEADER_TITLE_CATALOG; ?></a></li>
If you have ez-pages off for the footer, you will now have a <ul> with no items in it. I don't know how that will behave, and it might behave differently in different browsers as it is a nonstandard situation.