I have studied this issue with regard to many viewpoints. Here is a potential design plan based on googlemaps and my comments layered on it. Please study and submit you thoughts. I will be sending this to SMART at some point although right now it is only in draft form.
SMART needs to give the GGBTD some of it's ROW south of Larkspur for ferry parking. In exchange it will get to run a track down through the GGBDT property and across SFD and into the parking lot and finally into the terminal. Also, it will get some room for tail tracks to store it's cars. Finally, it will get to build a yard office in the area. In addition, it will get some parking down there too.
Finally, ferry operations will be yoked to train arrivals. Thus, ferry will leave immediately whenever ferry arrives. Eventually, people will realize getting on train is better than driving to ferry.