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..).

Add Parent to List of Subpages

This code works well to display child pages of the parent page while viewing both the parent page and child page. It doesn’t apply the current_page_item CSS class to the parent while viewing it (and only it, not interested in it being applied while on the children) – any suggestions?