Thanks for this. I found that the local site name was hard coded in the CSSMenuWriter menu.php file:
$WA_localRoot = "/site_name/";
$WA_remoteRoot = "/site_name/";
So I changed it to this which fixed the menu issue:
$WA_localRoot = "" .$WAGLOBAL_localRoot ."";
$WA_remoteRoot = "" .$WAGLOBAL_remoteRoot. "";
The site name was also hard coded for the URL location of all the images used in the CMS, this was rectified by changing the URL path for each image.
Thanks again.