The biggest argument for his base being San Francisco is the correspondence itself, with the majority of the letters mailed in this region to the San Francisco Chronicle. Using the 'least effort principle', in that people are generally lazy and usually perform a task closer to home, when at all possible, this could apply to the Zodiac Killer when mailing his letters. One alternative suggestion was that he lived across the bay and worked in San Francisco and this is equally plausible, however for the purposes of this argument we will leave that one behind.
We are fairly certain the Zodiac Killer used a vehicle to depart the scene in his first three attacks, but in the Presidio Heights murder of Paul Stine there is much doubt, some swear he had a getaway car waiting nearby, while others suggest he may have lived close by. What we do know, is the Zodiac Killer fled the scene on foot and claimed he entered the park and for the purposes of this article we shall take everything the Zodiac stated at face value and see where it leads us.
The Zodiac stated "I am the murderer of the taxi driver over by Washington St + Maple St last night." and if this was originally his intended murder site, then an exit up Spruce Street into the park is definitely closer than where ultimately the taxicab was found.
The Zodiac stated " 2 cops pulled a goof abot 3 min after I left the cab. I was walking down the hill to the park when this cop car pulled up + one of them called me over + asked if I saw anyone acting suspicious or strange in the last 5 to 10 min + I said yes there was this man who was runnig by waveing a gun & the cops peeled rubber + went around the corner as I directed them + I disappeared into the park a block + a half away never to be seen again." This description tallies with Spruce Street, which is situated approximately a 'block and a half away.' from the Donald Fouke and Eric Zelms sighting.
The Zodiac stated "The dogs never came with in 2 blocks of me + they were to the west." Arguello Boulevard, where Zodiac described the police cars and fire trucks and where the hive of activity was focused, is just over two blocks west of Spruce Street.
And finally Zodiac stated "there was only 2 groups of parking about 10 min apart then the motor cicles went by about 150 ft away going from south to north west." The only view of Arguello Boulevard from Zodiac's position in the trees adjacent to Spruce Street, is the section of road running northwest. In fact it runs from south to northwest, just as the Zodiac stated. In fact if he was concealed in the trees by Spruce Street, then everything he said would effectively be true. The reason the Zodiac only has an eyeline on this section of Arguello Boulevard, is that the rest is masked by trees, as it was in 1969. Here is the depiction once again before we continue.
So again taking the Zodiac Killer at face value we shall look in this region of Cow Hollow or the Marina District for basement residences and flood plains in the region. The 'My Name is..Letter' could easily have been telling the truth also. It was mailed on April 20th talking of "rain we had a while back." San Francisco's rainy months are between November and April, averaging over 100 mm monthly. Here is the chart. If you take a look at this historical monthly and yearly rainfall map of San Francisco, it is evident that December and January were particularly heavy monthly rainfall totals in 1969/70 compared to the average, bearing out the Zodiac's claim of being 'swamped out a while back.' http://ggweather.com/sf/monthly.html
But equally, if he had a vehicle on stand by, his journey may well have been relatively short also.