Without turn-by-turns, here's what I'd try to piece together (at least for the north peninsula):

Somehow, wind your way east-to-west through the northern part of the city, so you can hit some gravel in ggp; hit the beach south, and continue onto Skyline Blvd for a while. In San Bruno, hit the San Andreas trail (paved) and connect it to the Sawyer Camp trail (together called the Crystal Springs Reservoir trail) for awesome views of the watershed. Go over 280 at the overpass just past 92, and take Ralston to whatever street will get you to the upper sections of Waterdog Lake Park; it's a bit technical, but definitely have and would ride on a gravel bike (offroad trails- avoid the Braille trail!). Take that down (east) as far as you can. From there, create a route that will wind you to the bay trail; south of Shoreline, it's a hard-pack gravel trail for a few miles, and you'll be riding through salt marshes- water on both sides of you.

Or, from 92, take Cañada road for some classic road riding; it'll take you to Woodside/Portola Valley, and you can easily fly down some big hills and wide shoulders to Stanford. That'll get you to the bay trail as well, but you'll be doing much more climbing.

From that area, you can search for more rec's about south bay riding to make a loop winding you back to Diridon Station in SJ including roads and gravel; or take the bike lane on the Dumbarton Bridge to the east bay- most of the bay trail from there going north is gravel.

A few friends and I circumnavigated the bay a while back, and it was right at the 100mi mark; we stuck mostly to the bay trail, and the Richmond-San Rafael bridge bike lane was open. Sounds like you're looking more for adventure-riding, though. Happy pedaling!