As Palo Alto moves ahead with its ambitious and expensive effort to redesign three local rail crossings, city leaders are confronting a major obstacle: uncertainty over whether their chosen alternatives will pass muster with Caltrain, which owns and oversees the rail corridor.

To address this uncertainty, the City Council agreed on Monday to hire assistants who are particularly well suited to resolve these questions: Caltrain staff. The council voted on Monday to pay the rail agency $106,676 in exchange for assistance in refining local plans for grade separations, the reconfiguration of rail crossings so that tracks would no longer intersect with local roads. The council is now narrowing down its options for the three crossings at Churchill Avenue, Meadow Drive and Charleston Road.

The service agreement is intended to help Palo Alto navigate the complex, dynamic and highly technical landscape on a project that has been in the works for nearly a decade and that has already cost millions of dollars in staff time and consulting fees. While the council has gradually narrowed down its list of design options from more than 30 to five, it remains far from a final decision.

The final design may hinge on factors beyond the city's control. These include the configuration of a future high-speed rail system, which may require four-track segments; Caltrain's own design criteria, which would determine the length and steepness of any future train trench; and the ongoing electrification of the rail corridor, which is prompting Caltrain to revise its engineering standards at the same time as the city is pondering its grade separation options.

Currently, the council is looking at two alternatives for Churchill Avenue. Its preferred option is a partial underpass that lowers Churchill under the tracks and allows drivers to turn on Alma Street. If that proves infeasible, the council would consider closing Churchill and constructing various road, bike and pedestrian improvements.

On Meadow and Charleston, which are being investigated in tandem, the city considering a trench, an underpass and a "hybrid" alternative that combines raised tracks and lowered roads. The council's Rail Committee is scheduled to discuss these alternatives at its May 23 meeting.

So far, the city has relied largely on the consulting firm AECOM and its subcontractors to manage the various technical studies associated with grade separation designs, though staff from Caltrain have regularly provided the Rail Committee with updates about ongoing projects such as rail electrification and replacement of the old bridge at San Francisquito Creek.

The new service agreement formalizes Caltrain's involvement in Palo Alto's design process and commits agency staff to reviewing the city's tentative grade separation designs. According to the agreement, the budget and schedule for Caltrain staff time "is reflective of the level of support required during this early phase of the project," according to the agreement. It will address such questions such as the curve of the track alignment at Palo Alto Avenue, the vertical clearance standard and the thickness of the bridge deck.

"The level of Caltrain involvement is based on Caltrain's assessment of the project's scale, complexity, and the specific requests expressed thus far by the City of Palo Alto in previous correspondence to Caltrain," the agreement states.

The Rail Committee had vetted the proposed at its April 26 meeting and voted unanimously to approve it. Nicole Soultanov, deputy chief of planning at Caltrain, told the committee that the agency also has service agreements in place with other Peninsula jurisdictions, including Menlo Park, Mountain View, Burlingame and South San Francisco.

"Working on an operating railroad is like an open-heart surgery – you need to keep the patient alive and functioning well," Soultanov told the committee at the meeting. "So for Caltrain staff it means that we need to coordinate multiple projects simultaneously while ensuring that all our systems are in a state of good repair and our service keeps running at an appropriate level."

Because Caltrain staff time is necessary to implement local grade-separation projects, Caltrain uses a cost-recovery model and service agreements to allow the agency to work with cities.

The committee agreed to move ahead with the agreement, which members agreed is necessary to advance the city's efforts on grade separation.

"It's not like we have any other choice and we can talk to four other bidders on this thing," Rail Committee member Ed Lauing said during the April meeting.

The council unanimously approved the service agreement at its May 22 meeting as part of its "consent calendar," a list of items that advance with no discussion.