Let me first make sure I understand the issues you are having on these other two sites. Are you seeing active redirects or spam links on these webiste or just the warning that they may contain harmful content?
If it’s just the warning then that just means your sites are blacklisted. Google and others cache your pages and may warn visitors about malware that you have already cleaned up. You need to go to your Google Webmaster Tools and Request a Review of your sites to get them off the blacklist so that warning goes away.
If you are seeing active malware on these site or Google Webmaster Tools displays infected URLs with a date that was after you cleaned them then you can send me your WP Admin login for that site and I will check it out.