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WorkOS
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To ensure SSH and other security related things are configured correctly, you can take a look at DevSec which helps you to apply proven security configuration principles. Also there is guides like "Secure Secure Shell" which can help you to better understand what you can do to increase the security of your servers (this one is from 2015 but many aspects are still relevant).
I personally use a Personal Knowledge Management (PKM) system and my app stack is in there. I use Obsidian which is a md note-taking app. I have a note per VM, a note per service (db, smtp, vm security, webserver, etc...) that i link to the servers i use them on... Each server note has its technical desc, hosted services, whether i ise docker or barebmetal, the list of internal ips used, list of ports dedicated to each service. I made a note with CLI commands i want to keep in mind & another note with app ideas to self host. For diagrams, i used yEd which is an industry-grade free software. Not too bad!
I recommend documenting stuff on something like Wiki.js - it supports Mermaid and now even Diagrams.net (Draw.io) directly, making it easy to edit and add diagrams.
Sounds great! If you're looking for something like Obsidian, but a little different, check out Trilium as well ;)
All your files are local and in case you want to sync to multiple devices, there's Self-hosted LifeSync, I use that since weeks, works like a charm with a self-hosted CouchDB in the background.
A level above that is Kubernetes. Yes, K8s has a steep learning curve. Yes, K8s wastes a lot of resources. But if you can get past those downsides, it turns your Server into an "appliance". You say "here, run this", and it does. K8s very cleanly de-couples "applications" from "configuration" from "data" from "operations". For home users, I recommend K3OS. The OS has no moving parts -- in fact, it's read-only. It's just a quick way to get Kubernetes.