Did you launch a malware scanner with Timeline set to 10000 and also the deep scan enable? This will allow you to look for malicious files into your filesystem.
If you get alerts alerting you of XSS attacks mean all that hacking attempts have been blocked, so maybe google and others blacklisted your website for another reason. Do you have the file integrity feature enabled? If so you will be alerted of every new/modified file.
There is a complete use guide under Documentation section of the forum. If you need more help to clean your site I can do the work; please, use a different email to contact me because your current email is rejected because it appears in spam lists.