It seems very strange that Bob Vaughn's handwriting was the most closely matched to Zodaic's. What if Zodiac knew Bob Vaughn and asked Vaughn to write the letters?
It seems most plausible that Arthur Leigh Allen is the Zodiac, so going off that theory...
Arthur Leigh Allen expressed his love for the book 'The Most Dangerous Game' so if a viewing of this film was to be shown in a theatre near Allen then there is every possibility that he would have gone to see it. In the movie Bob Vaughn shows a keen interest in the movie (assuming this is correct) Allen and Vaughn may have got to talking that night and formed an alliance (this does not seem so unusual as he had also entrusted in Don Cheney with his whole Zodiac plan). The airing of the film in May 1969 was just 9 weeks before the first Zodiac letter meaning it would have given Allen and Vaughn ample time to become friends and discuss a plan.
It could also be that Arthur Leigh Allen simply copied Vaughn's handwriting to write his letters (it is relatively easy to mimic someone's handwriting with time and a lot of writing samples). Bob Vaughn wrote the posters for the theatre so, therefore, there would have been ample writing samples for Allen to have copied from.
What do people think?