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They would have to choose between Fishermans Wharf or the Marina. To properly serve the Wharf you would have to tunnel north of Bay St. and that's considerably north of the central Marina, typically Fillmore and Lombard Sts. Tunneling to Kirkland Yard and ramping to the surface seems most likely to me.
Now they missed their chance had they proceeded along 3rd & Kearny thence west on Columbus to Broadway and under the Tunnel to Broadway & Van Ness. From there a deep bore to Lombard & Fillmore. Too late now.