Nobody knows for sure the exact process in which the Zodiac Killer crafted the three ciphers mailed to the San Francisco Chronicle, San Francisco Examiner and Vallejo Times-Herald, but one possibility is that the author wrote the message first and then transferred it to the chosen grid formation, with the intention of leaving a number of spaces to insert his identity at the end of the cipher - a signature of sorts. The killer actually stated this: "I want you to print this cipher on the front page of your paper. In this cipher is my idenity."
We now know his identity as the 'Zodiac Killer', so one may expect to see 12 unsolved characters remaining at the foot of the cipher. He could have signed off the cipher with the wording 'Zodiac Killer' or 'I am the Zodiac', but either way, he would have had to leave himself 12 available spaces to complete the entire grid of 24 rows and 17 columns. The reason for believing he intended to leave 12 characters for his identity, rather than 18, is that he transferred the message from draft to grid incorrectly, actually omitting one important word - people.
The author had just switched from cipher 2 to cipher 3 (see below), which may have instigated the error.
In the trinity of letters to the newspapers, the Zodiac Killer described the inevitable consequences of not printing his ciphers.
To the Vallejo Times-Herald, he wrote "I will cruse around and pick of all stray people or coupples that are alone then move on to kill some more untill I have killed over a dozen people."
To the San Francisco Examiner, he wrote "If you do not print this cipher, I will go on a kill rampage Fry night. This will last the whole weekend, I will cruse around killing people who are alone at night untill Sun Night or untill I kill a dozen people."
To the San Francisco Chronicle, he wrote "I will cruse around all weekend killing lone people in the night then move on to kill again, until I end up with a dozen people over the weekend."
With regards to his threats, he used the word "people" no less than six times, so it was probably unfortunate that this was the word he mistakenly dropped from his grid when transferring the message to it.
The murderer wrote in the cipher "the best part of it, is that when I die I will be reborn in paradice and all the I have killed will become my slaves." It is highly likely that he accidentally reproduced his message incorrectly and failed to include the word "people" in the resultant cipher. The cipher should have read "the best part of it, is that when I die I will be reborn in paradice and all the people I have killed will become my slaves."
Since "killing", "kill" and "people" were routinely written 'hand in glove' in all the three newspaper communications, then it is no great leap of faith that the two words should have been bound together in the cipher as well.
In the San Francisco Chronicle portion of the cipher below, I have added "people" into the grid, thereby shifting the cipher across six spaces. The resulting cipher now contains 396 characters of legible text, leaving only 12 unsolved characters at its foot. The 12 characters we discussed earlier, in which the author had reserved for his identity or pseudonym. Signing off with the 'Zodiac Killer' or 'I am the Zodiac'.
However, the Zodiac Killer had made an error, accidentally omitting the word "people", and consequently had to improvise by using a combination of 'Zodiac Killer' and 'I am the Zodiac' to enable full use of all 408 spaces on the 24 X 17 grid. He may have settled for 'I am the Zodiac Killer', thereby satisfying the 18 spaces he had inadvertently left himself.
The idea of a 396 letter message (including "people" within it) would have negated the possibility of creating 30 rows by 13 columns totaling 390 characters - which is why he didn't do it. Therefore, he opted for 17 by 24, creating the grid we have been accustomed to.
What methodology he employed to encrypt these final 18 letters is another matter entirely.