SAN FRANCISCO — A state Superior Court judge this week handed down what appears to be a new roadblock to California’s bond-financed high-speed passenger rail project.

In a case that challenged the California High Speed Rail Authority’s final program environmental-impact report for a key segment of the planned San Francisco to Southern California system, Superior Court Judge Michael Kenny ruled that portions of the report were inadequate, raising the specter of delays if the authority has to rework its environmental documentation or change a substantial segment of its planned route.

California voters in 2008 authorized a $9.95 billion general obligation bond measure as seed money for the authority’s plan to build a high-speed rail system to operate 220 mile-per-hour passenger trains linking San Francisco with the Los Angeles region.

The key issue brought up in the lawsuit involves the 31-mile segment planned from San Jose south to Gilroy.

According to the Sacramento Superior Court ruling, posted online by a project advocate at his California High Speed Rail Blog, Judge Kenny agreed with arguments that the authority erred because its environmental impact report presumes that the high-speed trains will follow the existing right-of-way of the Union Pacific freight railroad, even though the UP, before the report was released, submitted letters to the rail authority indicating that it is not willing to share its right of way.

“If Union Pacific will not allow the authority to use its right-of-way, it appears it will be necessary for the authority to obtain additional right-of-way outside of this area, requiring the taking of property and displacement of residents and businesses, However, none of this was addressed” in the report, Kenny wrote.

There are six plaintiffs in the lawsuit, with a variety of motives, none of which directly have to do with the Gilroy Area.

The towns of Menlo Park and Atherton are involved because many residents of the wealthy San Francisco Peninsula communities north of San Jose don’t want to be disturbed by the high-speed rail project.

The four other plaintiffs are environmental and transit advocacy groups who have long opposed the so-called Pacheco Pass alignment that the high-speed rail agency has chosen to get between the San Francisco Bay Area and the Central Valley, preferring the more northerly Altamont Pass route, which would run through more densely populated communities there that would presumably benefit from improved rail transit.

The judge also agreed with the plaintiffs in ruling that the rail authority had failed to supply enough evidence to back its contention that the vibration effects of the high-speed trains will be “less than significant.”

Kenny sided with the High Speed Rail Authority in many other arguments brought by the plaintiffs, determining that the environmental impact report appropriately addressed issues that include ridership and financial projections, biological impacts, visual impacts, and land use impacts. Perhaps most importantly, the judge agreed that the authority had demonstrated adequate evidence to back its choice of the Pacheco Pass route over the Altamont Pass route.

A spokeswoman for the rail authority did not respond to a request for comment yesterday.

High-speed rail has taken on a much higher profile nationally under the Obama administration and as part of this year’s stimulus package.

This week, the Federal Railroad Administration received applications for the first portion of the $8 billion in passenger rail stimulus funding, which focused on improvements to existing passenger rail services for job-creation purposes.

California requested $1.16 billion for that portion, most of which would go toward improved trackage or equipment for its existing passenger train services.

The state did request $400 million toward construction of train facilities at the planned San Francisco Transbay station, which is the planned terminal of the high-speed rail line but would also benefit the existing Caltrain commuter service, which currently terminates about a mile out of downtown.

“By approving a nearly $10 billion bond in November, voters spoke loud and clear that rail, including intercity, commuter and high-speed, must play a greater role in addressing the transportation and environmental challenges we face in the 21st century,” Gov. Arnold Schwarzenegger said in announcing the state’s application. “On top of stimulating the California economy, federal investment in California’s rail systems will help lay a sustainable foundation for economic growth, help us meet our environmental goals and improve quality of life here in California.”

The second round of stimulus applications, focusing specifically on major high-speed rail corridor projects such as that proposed in California, is due Oct. 2.

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