In Mountain View, the biggest headache is actually VTA light rail. There's not enough room for six tracks side-by-side and elevated rail is not possible because of the nearby Shoreline, CA-85, Whisman and CA-237 overpasses. Something's going to have to give.

In terms of traffic and noise, the best solution would be to put both Caltrain/UPRR and HSR underground and keep VTA light rail at grade. However, this is also the most expensive solution, with possible subsidence risks (depends on geology and construction strategy). Also, UPRR diesel locomotives require large fans for ventilation and present a fire hazard. It's not clear if UPRR might be willing to switch to an electric locomotive for its Mission Bay Hauler trains.

Alternative 1: construct an underpass for VTA light rail, emerging back to grade as single track just west of the bike bridge and just south of the Caltrain right of way. This would separate the VTA light rail/Central grade crossing. Keep Caltrain/UPRR and HSR at grade, but with tall sound walls, either living walls or triple glazing rather than plain concrete in the downtown section. Note that these would shield the downtown area against noise from Central as well. Castro would become a deep underpass with no turnoffs onto or off Central. Motorists would need to use Shoreline + Villa instead.

Alternative 2: put only the HSR tracks underground, leave Caltrain/UPRR + VTA light rail at grade. Implement FRA quiet zone for the retained grade crossings at Castro and Central (VTA light rail). Sufficient room for HSR platforms.

Note that in all three scenarios, there's a potential conflict with gravity-drained conduits crossing the PCJPB right of way, e.g. Stevens Creek. It might be easiest to deal with in Alternative 1, since light rail vehicles can most easily cope with the steep gradients needed to run tracks under the creek.

It'll certainly make suicide by train quicker and easier.