Now try to build something through developed areas, maybe not at grade, and dealing with traffic rerouting, other infrastructure interruptions, and NIMBYism.
In Washington state we have laws that require workers to be paid Prevailing Wage, the premise of which is that working in a county pays the corresponding wage for a position based on the largest city in that county. The reality is often that the wage set is significantly higher than the true market wage, which causes costs to ramp up quickly. http://www.lni.wa.gov/TradesLicensing/PrevWage/WageRates/def...
Do you have a source for this assertion?
Elevated railways still need land purchasing for the land you're building on top of. Tunnels are way too expensive to be an alternative to surface construction even with land acquisition considered. And you need to punch through two mountain ranges, to get from SF to the Central Valley and then back to LA.
IIRC JR and TGV both expressed interest in a privately funded CAHSR, but balked at the Central Valley alignment.
I know I'm not from Cali or anything, but it's actually quite a bit worse than that. In California I'm almost positive it would require some tunneling. And not the easy kind of tunneling that you might see in, say, western North Carolina, asheville area. No. I'm talking about the hard kind that has to keep globally significant fault lines and seismic activity in mind.
There's also a tendency in big projects to be intentionally obtuse, come up with a number that the customers (tax payers) won't riot over, and then rely on sunk cost and other fallacies to let the project expand to its real size later on.