i think you are worrying about nothing.
according to microsoft the "SSL Certificate Settings created by an admin process for endpoint" events are normal and require no action:
https://learn.microsoft.com/en-us/previous-versions/windows/it-pro/windows-server-2008-R2-and-2008/cc727876(v=ws.10)?redirectedfrom=MSDNyou can do a google-search for "SSL Certificate Settings created by an admin process for endpoint" to dig up more information.
the files that were flagged were only flagged while being scanned by the malwarebytes program, not while being scanned in the normal manner, and all of the detections were "gen" meaning heuristics meaning only suspicious, not definitely malware.
as for not being able to make secure connections to some websites, my guess is that the only difference is that your browser is NOW requiring secure connections, which is a new thing. you just weren't seeing the message before about not being able to make a secure connection to particular websites because the browser wasn't requiring a secure connection, before.
also, you might need to update your bookmarks. it is possible that your bookmarks are set to open webpages with http rather than https.
