Certs not running & website became a mess

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It's quite possible that the wp-admin redirect loop is happening because you are proxying nginx->Apache, and WordPress is not detecting SSL properly.

The usual fix to that is to set x-forwarded-proto header at the nginx proxy:

proxy_set_header X-Forwarded-Proto $scheme;

and then in your Apache configuration, read that header:

SetEnvIf X-Forwarded-Proto "https" HTTPS=on

In the meantime, you can revert the HTTP-to-HTTPS redirect. That will allow you experiment until you get everything working on both versions of the site:

Change the port 80 virtualhost to:

server {
  listen 80;
  server_name yppgi.org www.yppgi.org;
  location / {
    proxy_pass http://192.168.99.101;
    proxy_http_version 1.1;
    proxy_set_header Upgrade $http_upgrade;
    proxy_set_header Connection ‘upgrade’;
    proxy_set_header Host $host;
    proxy_cache_bypass $http_upgrade;
    proxy_redirect off;
    proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
    proxy_set_header X-Forwarded-Ssl $scheme;
  }
}

Reload nginx, and try open your site in private browsing without HTTPS.

Yes.