What a cool article. It explains exactly why planners put off dealing with HSR and the Grapevine.
In my mind, I would start there to get over this giant hump as the first and most difficult leg of the engineering. There is a big issue of planning a rail system through LA with feeder stations ideally down into Long Beach and then Orange county. It probably wouldn't be high speed as 200mph, but at even half that, would be great.
Once you get to the Central Valley there are still hard choices. Basically from Bakersfield to Sacrament, most of the population developed along the route 99 corridor with 5 located some twenty to forty miles or so west. 5 intersects 120 at the bottom of Altamont Pass. 120 then continues west through Manteca by pass to meet 99. These intersections cause heavy traffic and traffic jams
The design of the California section should probably include a mixed rail systems running from San Diego to Redding and work with Oregon and Washington to make a complete system from San Diego to Seattle.
Well magic planning....
CG