WordPress Index Multisite Fail

I have been using a multisite install for several years. All of a sudden it is completely broken. Cannot see new users, all posts come up with permalink “basic inf”, Cannot see pending comments, no sites can edit posts, sites mark my static domain a hack then turn around and are fine, heartbeat errors (I added a heartbeat time limit plugin.)

I recently added Wordfence plugin and WP Super Cashe. I also enabled free version of Cloudflare. I just switched hosts also. Problems may have started just when I switched and I enabled those plugins and cloudflare just before leaving old host. I have no old files for sites to go back to at this point. I turned off the Templatic Publisher theme and all associated plugins on main site when I deactivated all plugins, and put site on a basic wordpress theme 2015. No help.

I have done everything. Disabled all plugins except domain mapping, checked the.htaccess files, dumped and reloaded wpsupercashe so it points to new host. The support at host has done everything they can with config files, .htaccess, checking for hacks, you name it. They said at this point it is a developer issue that is beyond their capabilities.

The new host reloaded a backup from 9/27/2016, the oldest they have from transfer of hosting and saw no issues until they tried adding a post and it started all over again.

At this point I will have to dump all three multisite websites and rebuild it all from original files from scratch one step at a time. These sites have worked for years with only minor issues until now. Something is really broken somewhere in the code or indexing and completely hosed.