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Do these steps below to get your site stabilized first and then I will assist you with setting up BPS Pro on one of your sites to make sure that there is not some sort of server compatibility issue or something deeper like that going on. BPS Pro setup is quick and simple in most cases so if extensive problems are going on then there is some sort of deeper issue going on.
1. FTP to your website and delete your root and wp-admin .htaccess files.
2. With FTP check your wp-config.php file and if you see WP Super Cache code in your wp-config.php file then delete it.
3. Login to your website and go to WordPress Settings >>> Permalinks and resave your Permalinks.
At this point there should be no traces of either BPS Pro or WP Super Cache left behind on your website. Let me know if you are still seeing errors and problems.