One simple thing that could be done to bring that CAHSR project down to somewhat reasonable costs would be to avoid palmdale. The Tunnel from Palmdale to Burbank will cost by itself a staggering 24 billion dollars.

I would also avoid Merced and focus on connecting to Gilroy from Madera and Caltrain Electrification from San Jose to Gilroy. The land in the I-5 pass isn't completely flat, but is much less rugged and wouldn't need tunneling.

Gilroy to Madera is approximately 84 miles and LA to Bakersfield via I-5 is 110 miles, at current construction cost of 100 million per mile you could build that for 19.4 billion dollars. At lower construction costs of 50 - 80 million per mile, you could build that from 9.7 billion - 15.5 billion dollars.