Building a light rail line through the heart of the Twin Cities is turning out to be way harder than anyone imagined. If the Central Line is to open by 2014 and stay within its $941 million budget, then miracles have to start happening.

Negotiators reported no miracles on Thursday in trying to settle a dispute that, if unresolved, could trigger a University of Minnesota lawsuit against the project. The U fears that vibrations and electromagnetic interference from trains may damage sensitive research laboratories located along the line’s Washington Avenue route. It wants not only technical changes to reduce possible damage but assurances of remedies for any damage that may occur in the future.

Metropolitan Council spokesman Steve Dornfeld emerged from Thursday’s four-hour session sounding like a diplomat: “Significant progress was made on several key issues. We’re hopeful that the project can go forward while affording the University the protection it needs for its research facilities.”

Council Chairman Peter Bell would have no comment, he said.

The sides missed a Dec. 15 deadline imposed by Bell but will meet again on Wednesday. It will be the 21st time the sides have met on LRT issues, Dornfeld said. He estimated the cost of the technical changes sought by the U at $32.9 million committed to traffic and pedestrian features on campus.

Kathleen O’Brien, vice president for university services, agreed that progress had been made but declined to elaborate. The U’s top priority, she said, is achieving confidence that researchers can continue their work without disruptions.

The U dispute is only one of several that have placed Bell and the Central Line project in a bureaucratic vise. Various parties are taking bites out of the budget while time runs short on keeping the project viable for federal funding. The Federal Transit Administration has made it clear that lawsuits and other complaints, if left unresolved, would push the project off the front burner. Failure to get the Central Line into President Obama’s budget next year could jeopardize the start of construction next summer and push its opening to 2015 or later.

Bell settled a dispute with Minnesota Public Radio, which had built new studios on the LRT route in downtown St. Paul, then decided to seek mitigation for possible noise and vibration.

More troubling, perhaps, are the unresolved civil rights complaints from two St. Paul community groups, the Concerned Asian Business Owners and the Preserve and Benefit Historic Rondo Committee. The groups expect the Central Line to cause disproportionate damage to minority communities, and they want compensation. They accuse the Met Council of failing to address the issue in its environmental review of the project, as required by federal civil rights law.

The Asian business owners say they expect lengthy construction and the loss of curbside parking to harm Asian businesses disproportionately. The project’s environmental impact statement “fails to express even a general intention to establish a compensatory program to support or sustain businesses or services that are adversely impacted,” Gen Fujioka, a policy analyst for the National Coalition for Asian Pacific American Community Development, wrote on the group’s behalf. “Absent mitigation, many of today’s small businesses will likely be shut down during the three-year construction project,” he wrote. “The loss of the minority businesses in turn will undermine the vitality of the communities they serve.”

Fujioka doesn’t use the term “gentrification,” but it’s obvious that the Frogtown and Rondo areas fear that LRT will increase property values and make the neighborhoods unaffordable for many residents. The issue has a bitter history, especially in the Rondo neighborhood. Grievances are still felt in the African-American neighborhood that was split apart by the construction of Interstate Hwy. 94 in the 1960s.

(Bell’s family was one of those affected; the Central Line, in contrast, will not require the demolition of homes or businesses or the displacement of residents.)

Minority communities have watched the Council negotiate with MPR and the University and wonder when their day is coming. “The history of the [Central Line’s] development is replete with instances where the non minority and non low-income communities were provided with enhancement and mitigation not offered (or even discussed) with the African-American Community,” the Rondo group’s attorney, Thomas F. DeVincke, wrote in the formal complaint.

Rep. Alice Hausman, DFL-St. Paul, said that the Federal Transit Administration “takes these complaints very seriously.”

Dornfeld said that the council doesn’t see race as a factor in how the project affects businesses and neighborhoods along the line.

Indeed, it’s curious that while the civil rights complaints seem to blame the LRT line for running through disadvantaged neighborhoods, one remedy sought is additional stations. Various St. Paul groups want stations to be added at Victoria Street and Western and Hamline avenues. The problem is that adding stations also drains the project’s budget and slows the running time of trains between St. Paul and Minneapolis. Both of those factors lower the project’s cost effectiveness index (CEI), a threshold in evaluating a project for federal funding.

Hausman compared the problems of building the Central Line with federal money to being placed in a straitjacket. “You learn all kinds of things along the way that would make the line better if you could change them, but you can’t. You’re tied into decisions that were made 10 or more years ago. You can see why some cities have decided to build these things on their own.”

No one’s suggesting that the Central Line won’t be built. It’s the centerpiece of the metro area’s future transportation system. But, compared with the Hiawatha Line, designing and building Central has produced one migraine headache after another. The benefits of building a train line as close to riders as possible are huge. The intimate route down Washington and University avenues accomplishes that.

But proximity adds complexity. And complexity adds stress — especially when time, money and human patience are in such short supply.