I think the point most guides overlook consists of the internal semantics of using a Zettelkasten, Luhmann essentially used it to create a paragraph (Zettel) & subchapter (Zettel Sequence, but note they of course sometimes he'd not manage to fit an entire paragraph on one Zettel due to margin limitations) branching & branchable, recursively self-referential choose your own adventure hypertextbook, from which he'd then generate regular textbooks. Hence why he said that his books basically wrote themselves — to write a book, he'd 'just' enter the Zettelkasten, and copy out everything he'd already written there on the topic, picking between branches & branchings as he went back, forth & side-to-side within it. Hence why if one looks close, one can find Luhmann seemingly self-plagiarising paragraphs from books he'd previously written. I suspect a similar mechanic sits behind the (in this sense very ignorant) accusations of self-plagiarism against Slavoj Zizek.

As such, one might wish to instead consider using Hypertext Fiction tools for creating a Zettelkasten, such these two (proprietary software, Mac OS X only, unfortunately):

http://www.eastgate.com/Tinderbox/

http://www.eastgate.com/storyspace/

Note that there exists an EXTREMELY useful plugin for Tinderbox which implements Stretchtext:

https://natematias.com/stretchtext/

Now gimme a combination of what roamresearch.com does with the above, but using the data structure of Hode:

https://github.com/JeffreyBenjaminBrown/hode

But with support for zzstructure like hyperthogonality:

https://github.com/JeffreyBenjaminBrown/digraphs-with-text/i...

And secretly use the patching patches feature of pijul.org in the background so version control actually becomes sanely doable, throw in elastic tab stop support, and maybe an entire kitchensink in which someone let a mixture of ChrysaLisp, SmallTalk, Hazel, Scala 3, /r/nosyntax, Inferno, RINA, GNUnet, & every single proof assistant and theorem prover sit for a tad bit long, and then MAYBE we can stop living in the dark ages of computing.

(Yes I'm bitter)

P.S.: Identity Transclusion ≠ Instance Transclusion

P.P.S.: Birth & Death of Javascript, anyone?