I found it at this blog post :
http://missionmission.wordpress.com/2008/08/03/freight-trains-barrelling-through-the-mission/

SP’s *original* route into The City (as shown in the ridiculously oversized map collage) was that of the old San Francisco and San Jose RR, which cut southwesterly through SOMA and the Mission to Dolores & 29th (some at grade, some on viaduct), then went south through the Bernal Cut and out to San Mateo County through what is now Daly City, Colma, and South SF to Tanforan. SP took over the SF&SJ around 1870, as part of its growth into “The Octopus.”

The Bayshore Cutoff (what we know and love as the Caltrain route) was conceived by SP’s ownership early in the 20th century, and work on it was underway when the Great Quake struck. The tunnel are numbered 1-4 from Mission Bay southward; thus #1 runs from 16th to 22nd, #2 from 23rd to 25th-ish, #3 from Oakdale to Williams, and #4 from Salinas to Blanken. (I vaguely recall that there are unused bores at 2, 3, and 4. I do not know if they were ever in revenue service.)

As one poster already mentioned, the Western Pacific tunnel was a completely separate operation from SP and the Bayshore Cutoff. Then there’s the Ocean Shore Railroad, which actually followed Islais Creek more closely than the SF&SJ/SP route (roughly, Alemany Boulevard), but that’s a story for another day.

Why not use the Fort Mason tunnel? Well, it’s been abandoned for decades and would need a lot of work to bring it up to code. I’d go through it on a dare, but I wouldn’t dream of opening it up to free access without some serious retrofitting.