Suggested software for use case

[TRS-80]

I don't recommend it to very many people, but have you considered Emacs?

There is a big learning curve, it's true. It may take you some years to really grok it fully. OTOH, it can also be a tool you use for the rest of your life.

You seem like you are halfway there with zettel, notes, citations, etc. All of these things are supported in various Emacs packages, which brings them all into a consistent environment (Emacs).

TwisterOS is based on Armbian, there is currently some issue with not being able to boot from eMMC. I just got my PBP, so I hope to be able to dig into that issue ASAP. I'm pretty sure it used to work, so not sure what's going on there.

I am also an i3 user (on desktop), it works very well in combination with Emacs (especially running Emacs as a server, and then spawning emacsclient windows, which then open very fast). Tiling window managers are a different paradigm, but for some people (myself included) once you try them there is no going back.

Whether i3 or Emacs (both of which are quite different paradigms from other things you may be used to), I would encourage you to play around with them when you have time to be curious, and not when you are pressed for time to produce something (like some research, or a paper, etc.) which can ruin the experience. Both have tons of resources all over the Internet, you shouldn't have too much trouble finding them, but let me know if you are looking for something specific.