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A political feud has erupted between transportation officials in Sonoma and Marin counties, pitting some who want to use federal funds to widen Highway 101 along the notoriously congested Novato Narrows against others who want to expand a transit center in San Rafael.

Sonoma County Supervisor David Rabbitt issued a rare public rebuke of the general managers at the Sonoma-Marin Area Rail Transit authority and the Golden Gate Bridge district, who made a formal request last month for $18.2 million in federal funds long coveted by Sonoma County transportation planners.

SMART and bridge district officials want most of the money to go toward updating a transit hub in San Rafael to accommodate rail and bus service. Rabbitt, who sits on the boards of both agencies, said the bulk of the money should be used to widen Highway 101 south of Petaluma and help alleviate some of the worst traffic gridlock in the entire Bay Area.

Spending the money on future upgrades to the transit hub, he said Monday, was akin to a “transportation crime” when “you have 100,000 people stuck in traffic on a daily basis.”

Rabbitt, who also serves as chairman of the Sonoma County Transportation Authority, said the general managers of the two transit agencies gave him no advance warning before they sent a letter to state transportation officials seeking the federal money for their own interests.

“It’s a matter of communication, and I think in this case we failed miserably,” the supervisor said at last Wednesday’s SMART board meeting.

Rabbitt last week aimed his ire directly at Farhad Mansourian, SMART’s general manager, who sat across from the supervisor during Wednesday’s board meeting. Mansourian did not respond during the meeting, and in an interview Monday, he declined to specifically address Rabbitt’s concerns.

“I am not making any comments about my board member’s comments,” Mansourian said.

The dispute centers on a congressional earmark granted in 2005 to bring ferry service to Port Sonoma on the Petaluma River. That project failed to materialize, and in March, federal transportation officials released the $18.2 million earmark for a new use.

The funds must be used on transportation projects within a 50-mile radius of the port’s proposed location. Otherwise, it comes with virtually no strings attached.

Suzanne Smith, executive director of the Sonoma County Transportation Authority, called the funding a “once-in-a-lifetime” opportunity to get money for completing the Highway 101 widening project. Carpool lanes would be opened on a 5-mile stretch of the highway from the Petaluma River Bridge to just south of the Sonoma-Marin county line.

Sonoma County already has $14 million for the project. Rabbitt sent a letter to state transportation officials — who are facilitating the earmark process — requesting $15 million of the Port Sonoma funds to start construction. He proposed that the remaining balance of $3.2 million go toward the San Rafael transit center.

Rabbitt fired off his letter several days after Mansourian and Golden Gate Bridge district chief Denis Mulligan sent their own letter to the state seeking $12 million for the San Rafael center, with the remainder going for the highway project. The cost for initial upgrades to the facility, which serves 9,000 people daily, is pegged at $3.5 million. But Mansourian said Monday there will be future costs associated with the project.

He said the transit center will benefit residents of both counties because SMART trains and regional buses will meet and connect there to other destinations. Passenger rail service is set to debut later this year along the initial 43-mile segment from downtown San Rafael to north Santa Rosa. A 2.2-mile link to the Larkspur ferry terminal is scheduled to come online in 2018.

The public feud over the Port Sonoma money offers rare insight into the behind-the-scenes tussles over funds for transportation projects. Sonoma County officials thought they had the money to start the 101 widening last year before a massive decline in gas tax revenue killed matching funds for the project.

Officials with the three transit agencies long have pined for the Port Sonoma money. Their most recent meeting to discuss the subject, on March 27, included Smith, Mansourian, Mulligan and former Congressman Doug Bosco, who is an investor in Sonoma Media Investments, which owns The Press Democrat.

But efforts to reach consensus during that meeting again failed. Smith said her impression afterward was that the sides would continue to talk.

“We were still having a conversation,” she said. “While I had been clear about our needs for the 101 project, I didn’t realize we were to the point of submitting something to the secretary of transportation.”

Mansourian declined to comment on the timing of the letter he and Mulligan mailed on April 27, nor about any communications he may or may not have had with SMART board members prior to the letter. However, he noted that it was drafted two weeks after Sonoma County officials submitted an application seeking 80 percent of the Port Sonoma money for the highway project.

Mansourian made the case that he is simply following his mandate to find money for projects where he can, even if at times it means competing with regional transportation partners. He said at the very least the letter gets SMART a “seat at the table.”

Three conservation organizations, along with the U.S. Fish and Wildlife Service, also have expressed interest in the money.

“It would be great if us guys got to make this decision. What a wonderful world that would be,” Mansourian said. “But this is a competitive project.”

A committee with the Metropolitan Transportation Commission is scheduled to take up the issue Wednesday prior to the agency’s full board making a funding recommendation to the state. The cutoff for the federal deadline is Sept. 12.

Jake Mackenzie, a Rohnert Park city councilman who is vice chairman of the MTC and a member of both the SMART and SCTA boards, said Monday his desire is for the local parties to meet again to try and bridge differences. However, he declined to say how he would like the money spent.

“Frankly, I had hoped that we could work this conundrum out internally and not engage in dueling letters,” he said.

Assemblyman Marc Levine, D-San Rafael, who has proposed abolishing the MTC over what he views as bureaucratic ineptitude, said Monday he was “troubled” that SMART staff — meaning Mansourian — sent a letter to state officials without consulting with board members first.

Levine, whose district spans the area where both transit projects seeking Port Sonoma funds are located, said his choice would be to spend the money on widening 101.

“What is the quickest way we can ease the pain for commuters stuck in gridlock? I think the answer is completing the narrows project,” he said. “The other projects will occur in time as well.”

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