Graysmith worked in production at the paper. In addition to drawing cartoons he did many other things involving getting photos and artwork processed to print in the paper. One thing he did was photograph all the Z letters (and keep copies for himself).
The very first thing Graysmith claims he did regarding his own investigation into the Z case was interviewing the teen witnesses to the Stine murder, which we know for a fact thanks to Mike Rodelli's research is an outright lie (Zodiac, p. 194). The very next thing we find him claiming he did is asking Morrill in detail about specific characteristics of Z's writing, sometime between 6-16-1977 and 1-30-1978:
"Do you think," I asked Morrill, "that the cursive letter d's and checkmark r's are part of Zodiac's real handwriting?"
"I think so. He's been consistent."
"What about that unusual k?"
"At first we thought that was consistent, but he got away from it. He made it in three separate strokes instead of the more usual two," said Morrill.
It would appear that, if he's actually being truthful here, this incident then is the very first thing he admitted to doing regarding his own investigation. And isn't it curious that he's asking the expert on Z's writing about very specific points regarding said writing?
On 8-5-1978 (p. 217), he goes into detail about the 4-24-1978 letter:
Over vacation, I took a long look at the April Zodiac letter. The writer had correctly used double postage, inverted the stamps, printed "Please Rush to Editor" with a downward slant, placed the odd punctuation colon after "yours truly," used no puncutation after the salutation, and put everyone else's name but his own in lowercase. The letter contained Zodiac's strange spacing between words and letters and used a style of d and three-stroke k used in 1969.
If the new letter was a fake and was done outside of S.F.P.D., what sort of information would be available to a forger without access to the original letters?
I carefully clipped every letter and envelope reprinted in the newspapers to see just how much information the general public had been given about the writing of the letters. Most letters had never been reprinted; those that were were cropped or reduced in size. The author of the letters was someone who had seen all of the letters, since character formations not used for nine years were in the message. (emphasis mine)
On page 218, Yellow Book goes on to say:
If it were a forgery, no one outside of the police investigation could produce such a perfect copy, incorporating information never before released. For a jealous insider the motive would be to discredit Toschi. But the forger would have no way of knowing that the letter would ever be found false.
In the very next paragraph, he states:
The weather this evening was warm and a shaft of strong sunlight cut through the picture window. I laid out reproductions of all the Zodiac correspondence on the rug... (emphasis mine)
Interesting... and incriminating! By his own admission, in 1978, Robert Graysmith himself had in his possession copies of every single Z letter. His previous statements make it crystal clear that he had studied the peculiarities of Z's letters in exhaustive detail; the list of details regarding Z's writing and phrasing on pp. 313-315 leaves no doubt. The fact that he inquired of Sherwood Morrill very early on is pretty damning too, especially when we consider that, according to the reissue of Zodiac, p. 346, and Zodiac Unmasked, pp. 499-500, it was right around the time he first heard of Allen, and Allen was released from Atascadero on 8-31-1977.
Graysmith goes into detail about how he believed Z used a projector to disguise his writing (pp. 218-219) and, despite this "fact," he notices someone's (presumably Allen's) natural handwriting on 3-12-1980 and states (p. 277):
On the wall was a sign; the lettering, done with felt-tip pen, looked similar to the Zodiac printing. I would have to get a copy of the sign.
A month and a half later, on 4-25-1980 (p. 281), he goes on to say:
I decided to take another look at the poster in back with its printing that resembled Zodiac's. As I feared, it was gone. But as I turned away, I saw something that brought me up short.
Hanging slightly above my eye level were six clipboards with notes and writing on them. One of them had block handprinting on it in felt-tip pen that was the closest to the Zodiac printing that I had ever seen. The block printing was signed. It was signed by [Allen].
As an aside, it's interesting to note that, as late as 7-22-1984 (p. 305), Graysmith was still trying to get samples of Allen's handprinting, despite the fact that he claims Z used a projector to disguise his own handwriting. It's obvious he does not believe his own theory; it was put forth simply to "prove" the April 78 letter was authentic. The fact that he was trying to get samples of Allen's writing for at least 4 years and probably 7 proves this.
Getting back to the matter at hand, Graysmith decides to take a photo of the printing, and just in case it didn't turn out, he states (pp. 281-282):
My absurd backup plan, if the photo was a dud, was to make a copy of the note in felt-tip and tape it down to a brown clipboard exactly like the one in [Allen's] store. I would then go back to the store and make a switch with my copy. I knew I was a good enough artist that if I put the two side by side and moved them around [Allen] himself couldn't tell which was his and which was the one I brought into the store. (emphasis mine)
Graysmith finally admits in his own words that he can convincingly forge someone else's writing. And now all the puzzle pieces have fallen into place.
Graysmith first heard about Allen in July or August 1977. He begins studying Z's writing in detail, gets pointers from Morrill about it, is probably the only person outside of LE who has copies of every single Z letter ever written, and admits he can forge other people's handwriting. Not only that, being an artist, and considering his projector theory, he undoubtedly either owned or had access to everything needed to forge the April 1978 letter in the way he described how Z composed it.
And what would he have to gain by this? It's apparent that either Graysmith or Toschi (or both) believed Allen was Z and SFPD couldn't prove it, so perhaps Graysmith believed the ends justified the means and forged the April 78 letter specifically to point at Allen, especially by using the phrase, "I am back with you." I am not suggesting that Toschi knew of and condoned the forgery, but that Graysmith, quietly and on his own initiative, thought he'd help things along and hopefully Allen would be arrested for the Z crimes, despite the fact that he manufactured the "proof" the cops could never find. However, it backfired, since it was discovered to be a forgery almost immediately, it cost Toschi his job in homicide and his reputation, and it made Morrill look like a fool.
Does any of this prove that Graysmith forged it? No. Are my suppositions accurate? Who knows... but the fact remains that Graysmith's own words are very damning, and he had the means, the motive, and the opportunity.