Fundamental concept of HSR is that it *can* run on conventional tracks along with ordinary trains in terminal areas and other tight spots at reduced speed. That way you can concentrate on the areas where you get long high speed runs first, then come back and do the more difficult/expensive spots later.

Caltrain between SJ and SF is all at least 2 tracks now, and 3 in spots. Adding an "express" track through more stations or perhaps all the way, with suitable grade separation in general and ped overcrossings at stations would allow both HSR and "Baby Bullets" to run through stations at a decent speed. Amtrak does that in the NEC, as do all the European and Japanese HSR systems. Stopping on the main line is something that only commuter, transit, and third-world passenger operations in light-traffic situations (alias most of Amtrak) do.

I looked at some of the EIR stuff at the HSR web site. Not a lot of detail - looks like they want to follow 58 over Tehachapi. That might be a bit difficult in spots if they want to keep the grade compatible with decently high speeds while dealing with - um - mobile geography (faults and landslides). Current UP/BNSF line is almost 3% grade even with a lot of curves and of course The Loop; highway hits 5% in spots and averages 3-4% on the main part of the climb; electric HSR can certainly handle some steep grades (4% or so), but not for more than a couple of miles without a big slowdown and special handling. Most of the other environmental subjects were done at a similarly broad level of detail. As a conceptual/feasibility/gross alternatives study, it served its purpose (order of magnitude costs and impacts, subject of course to inflation), but there's a lot of work still to be done to flesh it out to where somebody could actually build something.