Plagued by years of funding shortages and spiraling costs, California’s beleaguered high-speed rail project suffered another unexpected blow this month in a new report that more than tripled the cost estimate for the San Francisco-to-San Jose segment to a staggering $5.3 billion. The new price tag is part of a report that completes a years-long environmental clearance process for the 48-mile corridor that would carry bullet trains down the Peninsula on electrified Caltrain tracks at 110 miles per hour and eventually on to Southern California. It outlines three stops, a controversial rail yard …