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Two decades after the concept of bringing commuter rail service to the North Bay started gathering steam, the first set of trains operated by the Sonoma-Marin Area Rail Transit authority pulled into the Cotati station Tuesday to cheers from hundreds of spectators.

Skeptics doubted whether such a day ever would arrive, given the myriad financial and regulatory hurdles the rail authority had to overcome to reach the historic milestone. Significant questions remain prior to passenger service starting, currently set for December 2016.

But on Tuesday morning, beneath stormy skies, such doubts were mostly set aside as two gray and green rail cars bearing the SMART insignia pulled into the packed station with horns blaring.

“It wasn’t that long ago that people were saying this project wouldn’t come to fruition,” said Rep. Mike Thompson, D-St. Helena. “And now, it is.”

Seated inside one of the rail cars, Sonoma County Supervisor David Rabbitt, a member of SMART’s board of directors, acknowledged the rail agency’s “trials and tribulations,” which he said have included issues with the electorate and construction delays.

“But seeing this car really lets you know that this is moving forward,” Rabbitt said.

The debut of the diesel-powered rail cars comes two decades after a study that envisioned the service, 13 years after the state Legislature created the SMART district and seven years after voters in Sonoma and Marin counties approved a quarter-cent sales tax to fund the project.

Numerous challenges threatened to derail the project along the way, including funding shortfalls that forced officials to scale back the project’s initial scope, a threatened ballot initiative in 2012 that could have overturned the sales tax and disputes between city and county officials and SMART representatives over governance and planning.

Farhad Mansourian, the rail authority’s general manager, struck a defiant tone Tuesday after the hourlong ceremony, saying he “has no answer” for people who continue to doubt the rail service’s viability.

“I say, ‘Get on board,’ ” he said.

His enthusiasm was matched by Rohnert Park City Councilman and SMART director Jake Mackenzie, who said he has “every confidence” the rail authority will be operating passenger rail service by the end of next year.

That service initially will include a 42-mile segment from downtown San Rafael to north of Santa Rosa. SMART is planning to operate seven two-car units along the route, with officials saying it will take under an hour to traverse.

The slope-nosed cars, called Diesel Multiple Units, run in pairs, with the ability to have a third car added in between to increase capacity. Each car has 79 seats, with standing room available for about 80 people. The cars also feature space for bicycles, Wi-Fi service and, in some cases, snack and beverage bars.

Charlotte Shiffman, whose family lives in a condominium on Santero Way a short distance from the Cotati station, said she’s looking forward to hopping aboard the train with her three boys for adventures along the route. She brought along her 4-year-old son, Ronan, on Tuesday to check out the rail cars.

Alan Nelson, a Sebastopol resident who described himself as a semi-retired charter bus driver, also expressed enthusiasm about the new rail line.

“I’m really glad to see it’s finally here,” he said. “It’s going to help us with our traffic situation on Highway 101.”

The rail agency is pursuing $40 million in federal and regional funding to extend the line to the Larkspur ferry terminal.

SMART’s original plan to extend service north to Cloverdale lacks funding. Mansourian said that remains one of the rail agency’s most pressing concerns.

However, Cloverdale Mayor Bob Cox, who toured the new cars Tuesday with his wife, expressed optimism that the rail service will make it to the northern Sonoma County city “not only in my lifetime, but probably while I’m still on the City Council, should I be re-elected.”

Mansourian said another pressing issue for SMART is the completion of a bike and pedestrian path that was a key element of the rail project when voters approved the sales tax to pay for it. Bike advocates in particular have expressed dismay that the pace of construction on the path has lagged far behind the rail project.

Mansourian on Tuesday said the rail authority will have to rely on state and federal grants to complete the pathway, which to date has seen very little progress, other than short sections in the city of Santa Rosa and along Highway 101 from Olompali State Historic Park north of Novato to the Redwood Landfill overpass at San Antonio Road.

In February, the Rohnert Park City Council approved the rail agency’s request for an easement onto city-owned property that includes an additional 3,500-foot section of the planned bike path.

About 450 people packed the Cotati station Tuesday for the ceremony celebrating the new rail cars. Among the attendees were the North Coast’s two congressmen and numerous public officials from the two counties where the rail service will operate. Representatives from the Japanese manufacturer of the cars also were on hand.

The two cars, which cost $6.7 million, were developed at the Nippon Sharyo factory in Toyokawa, Japan, and assembled at the Sumitomo Corp. of America plant in Rochelle, Ill., to comply with the rail authority’s federal funding requirement to manufacture and assemble the cars in the U.S.

“The cars are built very tough, for any environment,” said Kevin Koyasu, chief executive officer and president of Nippon Sharyo USA.

The trains will travel a top speed of 79 mph. It costs about $1,000 to fill the 270-gallon tank on the cars, which get about 2 miles to the gallon, according to Tom Matoff, SMART’s operations manager.

The agency intends to run trains every half-hour during peak commute times with a midday train and weekend service. The rail authority estimates 5,000 riders a day will use the service.

Tuesday’s event also drew a handful of sign-wielding protesters who contend SMART is not planning to hire or train union workers from other Bay Area transportation systems. Protesters argued that violates a provision of the 2002 legislation that established SMART requiring the rail agency to create bargaining units representing such workers.

“They’re circumventing the law,” said Raymond Messier, president of the Amalgamated Transit Union Local 1575. “That’s no way to start a relationship.”

Mansourian could not be reached late Tuesday for comment on the union’s allegations.

Peter Calthorpe, a Berkeley urban design planner who drafted a transportation study in 1995 that helped outline the vision for SMART, said Tuesday by phone that the debut of the first rail cars was “very satisfying.” But he also said “it seemed to take too long.”

He said light rail systems in Oregon and Utah that rely on similar concepts of marrying transit with mixed-use development at stations are up and running, and exceeding ridership expectations. However, he said those systems, which rely on rail cars powered by electricity, cost more to develop and operate than SMART, which is relying on diesel technology more commonly used in Europe.

“What you are doing in Sonoma and Marin is important because it’s a more affordable form of transit that can be replicated around the country,” Calthorpe said.

The rail cars unveiled Tuesday initially will be stored on a side track at Fulton Road and River Road north of Santa Rosa during construction of the SMART maintenance and operations center at Airport Boulevard, which is expected to open in July. The trains should be a familiar sight, however, as they undergo more testing along the initial operating segment.

Mansourian said SMART will take delivery of a new set of rail cars every two months prior to the service starting next year. The rail agency’s $56 million contract with Sumitomo gives SMART the option to buy up to 80 train units.

SMART has added revenue by selling 12 train car options to a rail authority in Canada, and another option to the TriMet Transportation District of Portland, Ore., for $100,000.

The public will have more opportunities to tour the SMART rail cars at upcoming events in Sonoma and Marin counties, a spokeswoman for the agency said.

You can reach Staff Writer Derek Moore at 521-5336 or derek.moore@ pressdemocrat.com. On Twitter @deadlinederek.