The Army manual is a pdf so I had to do this as screenshots but this is a very clear description of what we are attempting to do with Kryptos.
You can also read some more about the semiotic definitions of code in an excerpt from the section on Code in the Handbook of Semiotics by Winfried Noth.
I discuss Kerckhoff’ Principle and Kryptos.
Here is a short bit about key choice.
I also blather on about the chance a code (not cipher) system was used in Kryptos.
I’m always working on re-learning probability as well.
I found a programming reference that sounds similar to K4: obfuscated code.
Continuing on the topic of modern ciphering, read about pseudorandom number generators.
There are a lot of papers out there but two that are relevant to CIA activities (the context of Kryptos cryptoanalysis) and worth the read are a paper by Christopher Felix and one by Charles J. Micoleau.