It is pretty easy to remove all persistent XSS attacks from PHP, just remove all instances of output functions (such as echo and print) with their safe counterparts from OWASP PHP Security Core Library, and then whenever you need HTML elements to be outputted, used the appropriate functions or PHP tags. There's a scanner in PHP Security Project that scans for this and can replace it effectively as well.
As mentioned earlier, you can download the Scanner PHP using the PHPSEC framework at https://www.owasp.org/index.php/OWASP_PHP_Security_Project
/** * Array to hold all the words that are considered unsafe. * @var Array */ public static $blacklist = array("T_ECHO"=>"echo", "T_PRINT"=>"print","printf","vprintf");