My scheme would still be to forget Marin entirely. Most Marin residents are incapable of imagining a world with real people and "mass" transportation.

Build a new RR line along Lakeville Hwy connecting to the existing line at Port Sonoma and Petaluma. Whether wired or not, run passenger service entirely within Sonoma Co. to a ferry terminal at Port Sonoma. Use diesel or electric MUs like Colorado Railcar sells (not light rail cars) to minimize effects on freight activity. Theoretically, you could even run a feeder rail service from Sonoma (and maybe a weekend "wine train"), though the potential ridership is too small to justify it (hardly enough even for buses) without some Locally Unwanted Land Use (LULU) changes. From there, boats (Vallejo-style) to SF and someplace (Richmond, Berkeley maybe) in the E.Bay where connections to BART can be arranged. Charge a premium for Marin passengers arriving by bus or car (special Marin rates for park & ride lot). Tear out the steel bridges and the rail for scrap, and sell the Marin r/w wherever decent-sized parcels remain to low-income housing developers. Tear out ALL the bridges, so if the trail people want to put something back in (say, at Novato Creek) they have to spend their money to do it. Then let Marin deal with the consequences when gas reaches $10 and diesel (for the buses) $12 (probably in less than 5 years).