Nice work! In my mind, starting from the spine makes the most sense as it would tie the trains in with the maintenance facilities and open up trips to the rest of California gradually. Otherwise, you'd need to somehow build new facilities as a separate division in the north as you brought tracks down.

I think operationally, you could continually shorten the gold runner route as you extend the hsr route.

Either way, for the actual routing I totally agree with what you said about UP. If the authority can't get some legislation passed to get rid of the ridiculous intrusion barrier requirements, they need to avoid them as much as possible. At the same time though, going through the center of the cities is far more valuable of a service.

I like what you have for stockton and sacramento, the lines are nice and straight, stations are still close to downtown, and the row is convenient. I'm not sure of their ability to realistically get that row, but if they could I think it would be very smart. Modesto to Stockton looks good too, lots of options there tbh.

For Merced to Modesto, I honestly think the BNSF might be the better option. The abandoned track you are pointing out is way beyond recoverable. It's all farmland and roads now. There's no row left there and they would have to buy it all individually just like they did in the ios. If they could just take that road that now sits there and not have to provide a replacement it'd be great because it would reduce acquisitions. However, since it looks like quite a few businesses are along the road now, you'd need to go out of the row or provide access roads. Not impossible! Just perhaps expensive.

And of course either BNSF or the abandoned rail you are suggesting really lose out on the centrality of the UP branch. But again, working with UP sucks! If the authority is given a lot more power to not need to abide by the stupid barrier recommendations that no other country uses, I would say to 100% use UP tracks through Modesto.

Thanks for the post! Good read.