We will only be working with HTML/blocks/block-Modules.php from here on!

If any other theme besides the one we are working on is selected, our changes should not be evident.

This is the part that fills in the table with our site nav links:

/* Now we make the Modules block with the correspondent links */

    $content .= "<strong><big>&middot;</big></strong>&nbsp;<a href="index.php">"._HOME."</a><br>n";
    $result3 = $db->sql_query("SELECT title, custom_title, view FROM " . $prefix . "_modules WHERE active='1' AND title!='$def_module' AND inmenu='1' ORDER BY custom_title ASC");
    while ($row3 = $db->sql_fetchrow($result3)) {
	$m_title = stripslashes($row3['title']);
	$custom_title = $row3['custom_title'];
	$view = intval($row3['view']);
	$m_title2 = ereg_replace("_", " ", $m_title);
	if ($custom_title != "") {
	    $m_title2 = $custom_title;
	}
	if ($m_title != $main_module) {
	    if ((is_admin($admin) AND $view == 2) OR $view != 2) {
		$content .= "<strong><big>&middot;</big></strong>&nbsp;<a href="modules.php?name=$m_title">$m_title2</a><br>n";
	    }
	}
    }

I am not going to mess with the rest! Only admins see it anyway.

So, let's make the above part conditional:

if ($ThemeSel=='yourtheme') {

    /* make modules block look like I want */

    } else {

    /* make modules block look like it used to */

    }

Make sense?

For now we are going to put the content the same in both places.
(except for the first $content line, which makes a "Home" link)
(your logo is a link to "Home", why do it twice?)

The result:

/* Now we make the Modules block with the correspondent links */

    if ($ThemeSel=='yourtheme') {
    /* make modules block look like I want */
    $result3 = $db->sql_query("SELECT title, custom_title, view FROM " . $prefix . "_modules WHERE active='1' AND title!='$def_module' AND inmenu='1' ORDER BY custom_title ASC");
    while ($row3 = $db->sql_fetchrow($result3)) {
    $m_title = stripslashes($row3['title']);
    $custom_title = $row3['custom_title'];
    $view = intval($row3['view']);
    $m_title2 = ereg_replace("_", " ", $m_title);
    if ($custom_title != "") {
      $m_title2 = $custom_title;
    }
    if ($m_title != $main_module) {
      if ((is_admin($admin) AND $view == 2) OR $view != 2) {
      $content .= "<strong><big>&middot;</big></strong>&nbsp;<a href="modules.php?name=$m_title">$m_title2</a><br>n";
        }
    }
    }
    } else {
    /* make modules block look like it used to */
    $content .= "<strong><big>&middot;</big></strong>&nbsp;<a href="index.php">"._HOME."</a><br>n";
    $result3 = $db->sql_query("SELECT title, custom_title, view FROM " . $prefix . "_modules WHERE active='1' AND title!='$def_module' AND inmenu='1' ORDER BY custom_title ASC");
    while ($row3 = $db->sql_fetchrow($result3)) {
    $m_title = stripslashes($row3['title']);
    $custom_title = $row3['custom_title'];
    $view = intval($row3['view']);
    $m_title2 = ereg_replace("_", " ", $m_title);
    if ($custom_title != "") {
        $m_title2 = $custom_title;
    }
    if ($m_title != $main_module) {
        if ((is_admin($admin) AND $view == 2) OR $view != 2) {
        $content .= "<strong><big>&middot;</big></strong>&nbsp;<a href="modules.php?name=$m_title">$m_title2</a><br>n";
        }
    }
    }
    }

Save and test again, you should see no new changes.

Now let's make changes!

Remove the two instances of <strong><big>&middot;</big></strong>&nbsp;from the
 /* make modules block look like I want */
section.

Save and test, you should no longer have dots before your links.