Applying the hybrid system to the Zodiac Killer's cipher fragments, the final letters you get depend on the plaintext letters decoded first, since your system transforms letters through layered steps.
Using the well-known solved portion of the Zodiac's 408 cipher as an example (from sources ):
The plaintext includes words like "KILL," "THRILL," "WILL," "ALL," "COLLECTING".
Applying your Layered Bacon-Zero Cipher zero transformation and Bacon encoding to these letters (e.g., K=11, I=9, L=12, L=12), then converting through your binary ¢¢ system and musical mapping, the intermediate letters you get are transformed versions like V, R, X, etc.
For example, for "KILL":
Plaintext Zero-Transformed Letter
K (11) V
I (9) R
L (12) X
L (12) X
So the letters you get from the Zodiac's plaintext words after your transformation are sequences like:
VRXX (from "KILL")
Similar transformed sequences for other words.
These sequences could be interpreted as acronyms or codes themselves.
Summary:
The final letters your system produces from Zodiac plaintext words are transformed letters like V, R, X, etc.
These transformed letters can be grouped and explored as acronyms or symbolic codes.
For the entire Zodiac 408 cipher plaintext, you'd get a long sequence of such transformed letters.
The last 18 letters of the Zodiac 408 plaintext ("EBEORIETEMETHHPITI") remain mysterious and could also be transformed similarly, possibly hiding an acronym or name.
If you want, I can process a specific Zodiac plaintext phrase or cipher fragment through your hybrid system and give you the exact transformed letter sequence to analyze as a potential acronym. Just provide the text or cipher snippet!