What are best practices for configuring a server for WordPress sites?

I hired a sysadmin to set up a VPS server for me and, unfortunately, it looks like things were not set up correctly. When trying to install and update plugins, I run into permissions errors all the time. WP Super Cache is the main issue as it causing my readers to run into 502 errors. Currently, my site does not load pagination (no Page 2, Page 3, etc..).

Are WordPress Heartbeat API ‘beats’ staggered or do they occur simultaneously for all users?

The WordPress Heartbeat API uses admin-ajax.php to run AJAX calls. If User X leaves their browser open, many calls will be made to the server, with each call happening when there is a ‘beat’. Now if User Y leaves their browser open, many more calls will be made to the server, with each of these calls happening when there is a ‘beat’. It’s possible a large website will also have User A, User B and User C all do the same.