I think building an underwater tunnel following the Carquinez Bridge would make better sense than trying to rebuild the 1962 Carquinez Bridge so as to accomodate rail. And the rebuilt Sacramento Northern between Pittsburgh and Sacramento would be the new rail line to divert freight from the Benicia-Martinez rail bridge (that too would also be replaced with a new bridge; this would require the freeway bridge to be rebuilt)
I'm guessing Part 3 (if there's gonna be one), would include completely new rail lines, such as the the Tejon Pass railway, which is absolutely necessary for connecting the San Joaquins as the Tehachapi is pretty much off-limits for future passenger rail, a new LAUS-Santa Ana rail line following I-5 (primarily for HSR), and a new rail line following I-680 from Martinez south to San Jose
As for the Benicia bridge, the replacement for the train bridge hasn't even been fully planned yet since there isn't funding available to do so. The plan is so unplanned yet, that the advocates haven't figured out that they would need a tunnel to connect Franklin Canyon to the Martinez Subdivision. A tube would also be asking for a bit much in that area. Something like that would have to be held off until full electrification, not to mention a bridge would be a bit easier to build than a tube.
As for Tehachapi Pass, BNSF and UP have added capacity to it over the last few years, so I wouldn't say it could never be used for passenger trains should the state get its act together. From looking at train maps, there are at least 12 tunnels in the pass which would be the biggest hurdle to double or triple tracking the line. Mostly given how expensive tunneling gets before you add geology into it. If triple tracking was offered, I doubt they would say no out right. I also wouldn't expect the number of passenger trains to get much beyond 14 round trips per day, also working with the assumption that 4 of which are overnight trains.
As for Tejon Pass, I wouldn't see it as something that is necessary if you can get concessions out of the railroads to use Tehachapi. And even then, it might not even be worth given other alternatives such as beginning to electrify the busier lines or adding lines somewhere else. Not to mention if the high speed line actually gets funded, it would absorb most of the ridership anyways. Which would make lower speed, day time trains less necessary.
As for an I-5 alignment, I wouldn't advocate any money from such a project to go to the high speed project. With how spineless politicians are, asking for any more money for the high speed project would make any ask for rail funds dead on arrival.
I-680 has been semi claimed by BART as one of its future projects. I would be willing to let them plan that on their own.
Also just to bring this up, I am advocating that the $23-$30 billion phase one be paid for without asking the feds for any money. Cause once there is $1 of federal money involved, everything has to go by their rules without question. So its not like the state would have limitless money to build certain projects like Tejon Pass. The state would have to ask the question of "where is this money have the biggest bang for the buck?" Like with using this idea, if it were to get into a legislative chamber, to ask for money for the high speed rail line (I-5 to Santa Ana) or projects that could be cast as purely a purely local concern (1-680 corridor) would turn this idea into a poison pill for even the most transit friendly Democrat. Right now, I am only figuring on expanding on existing rails and plans that are somewhere in the planning process.
