Sounds like you want a proper backup solution. Take a look at borg backup, a tool that supports encrypted, deduplicated, compressed, incremental backups. You can even directly save to your cloud via protocols such as ssh, s3, etc.
You already have a plethora of great suggestions for improvements to make, so I won’t leave any more, but rather offer some advice. It can be daunting to go all in and sacrifice the conveniences you currently enjoy. This is why I recommend you change your behaviour and software in a piecemeal fashion. Change only a few (or even one) things at a time and get used to it. Once you are comfortable with where you are at, then introduce more improvements. This approach will help prevent you from getting overloaded or burnt out, resulting in you going back and compromising your privacy. Good luck!
It depends how you use it. There is no requirement as to how you set up your directory structure, so you could have one file “passwords” with all your credentials in, including the website. That would break a lot of plugin’s functionality though.