I guess either of those possibilities could be true.
I have seen some speculation that the 18 symbols of filler at the end of the 408 have some undiscovered connection to the 340. Could the cipher author have started a new substitution key there, continuing it into the 340? Maybe, but the high number of symbols copied into the 18 symbols from the earlier rows of the 408 make them seem that they are only filler.
I also wonder if more plaintext is missing from the 408. Between the 2nd and 3rd parts, there is a break in continuity of the plaintext: [e I have killed will become my slaves]. The 3rd section of the cipher has more broken/interrupted homophone cycles (see this visualization), so it makes me wonder if restoring a missing section could fix up some of those interrupted cycles.
Straightforward "I will be reborn in paradice and all the people I have killed will become my slaves." seems to be most likely, but I have also pondered the possibility that more is missing. An entire line would make some sense regarding the presumed filler at the end. Or maybe some of the text of the last part was edited here and there. I have seen your write-up on it, it is very detailed.
A while back I deleted my dropbox contents and some stuff got lost, here are again the symbol placement pictures:
340:
408:
It is of note that there is extra spacing between row 12 and 13 in the 340.
Furthermore:
Interestingly, the smallest gap is between rows 13 and 14, which is right after the biggest gap!
Seems to indicate that Zodiac compensated for this.
Also, if you were to draw a horizontal line in the middle of each row, the dot symbol in all instances appears to be have been placed a little bit higher than this middle line. I am not sure why. Can someone conjecture from this? In other words, why is the dot symbol placed a bit higher, more to the top of the row?
Since there is more regularity in spacing between rows than between columns it is highly likely that the symbols were written out by row order. In other words, if you were to draw a line in the middle of each row and column, the symbols line up better with the row lines.
Another point towards the symbols written out by row order is the extra spacing between row 12 and 13 and then catching up between row 13 and 14 as previously mentioned.
I am uncertain about the dots but what’s interesting about your spacing observation is that it lines up perfectly with the bus bomb letter. On the first page of that letter he writes 12 lines then draws a line. I’ve always believed there’s a chance that Z created some sort of cheat box within the 340 by using the first letter of each line of the bus bomb letter. Never tested it in that area starting at line 13.
I see. What do you mean with a cheat box?
For Example: Let’s say some of the dots represent stopping points. Take the dripping pen letter and substitute the first letter of each word into specific areas of the cipher. Once complete you have a cheat box that can be used to decipher the top portion of the cipher. It’s obviously not a conventional way of solving and I have no idea if there are ways to test to see if the cipher was constructed in this manner. Just a thought in case you wanted to explore a different idea.
Probably just a coincidence but when putting together the above example, I counted 62 words on the Dripping Pen letter after "This is the Zodiac Speaking." And there are exactly 62 symbols that could be substituted assuming there’s any accuracy to the mirroring of the stippled dots.