The logoWrapper div is still active, with its trailing <br class="clearBoth" />.
Moving the logo div comment tags out to enclose the whole wrapper and break will remove that space:
HTML Code:
<!--bof-branding display-->
<div id="logoWrapper">
     <!--<div id="logo"><a href="http://endlesssonata.com/catalogue/"><img src="includes/templates/custom/images/" alt="" /></a></div >-->
</div>
<br class="clearBoth">
<!--eof-branding display-->
change to
HTML Code:
<!--bof-branding display-->
<!--new begin comment location<div id="logoWrapper">
     <div id="logo"><a href="http://endlesssonata.com/catalogue/"><img src="includes/templates/custom/images/" alt="" /></a></div >
</div>
<br class="clearBoth">new end comment location-->
<!--eof-branding display-->