Looking at that site, I would turn off wp-db-backup (scheduled backups can slow your site down) and trade out wp super cache for w3 total cache. You can safely remove the hotfix plugin from all sites now
I'm not familiar with the pix suite of plugins, so I can't speak for those, but the other plugins look fine to me. I also peeked at your other sites, and I think the issue may be the database, not the file server. I ran a DB optomize on all your sites and checked the plugins which seemed to pick up a little bit.
One of the sites is running RevSlider 4.3.8 - That needs to be upgraded ASAFP. That's a vulnerable version of the plugin and it's possible that's what's causing the slow down.
Looking at the VPS, I have a couple suggestions.
Check "Disable mod_php" - You're not using it.
Disable "Jabber Transports" - You're probably not using it either
I personally disable "FTP Server" which doesn't disable SFTP or SSH, but it's just safer than raw FTP.