Palo Alto has yet to begin reconstructing any of its four rail crossings, but it has already spent close to $3 million on consultants as part of its yearslong effort to figure out what exactly the work should entail.

And the bill is expected to climb significantly in the coming months as the city embarks on further analyses related to grade separation, which is the realignment of roadways from train tracks at rail crossings so that they no longer intersect. These include a geotechnical study to examine the feasibility of digging tunnels and underpasses under creeks, an evaluation of a potential four-track segment and various bike and pedestrian improvements near the tracks.

While the City Council has generally been in agreement when it comes to its options on the rail corridor, members were split earlier this month when they were asked to approve the latest addition to the city's contract with Aecom, the primary consultant on grade separation. On Feb. 14, the council narrowly rejected a staff proposal to add $722,170 to the Aecom contract, which would have raised the overall contract amount to $3.6 million.

Instead, the council voted 4-3, with council members Alison Cormack, Tom DuBois and Eric Filseth dissenting, to defer the decision so that its Rail Committee could delve deeper into the decision and determine which studies should be prioritized.

The three council members who dissented expressed concerns that failing to approve the contract amendment would hinder the city's progress on grade separation, which has been proceeding in fits and starts for more than a decade and which has accelerated in recent years. With Caltrain advancing its own plan to electrify the rail corridor and increase the number of trains moving up and down the Peninsula, various city councils have unanimously supported grade separation, a project that they see as critical to ensure safety along the tracks and to prevent massive congestion at rail crossings once train traffic increases.

The council made some progress in the effort last year, when it chose what's known as a "partial underpass" as its preferred alternative for the Churchill Avenue crossing and when it eliminated the viaduct from consideration for the two south Palo Alto crossings at Meadow Drive and Charleston Road. The council had also previously decided to shelve planning for the northernmost crossing, Palo Alto Avenue, which it is preparing to evaluate as part of a broader downtown plan.

One area that the council is hoping to further evaluate is the idea of building a trench in south Palo Alto, a popular alternative that has an estimated price tag of about $800 million, according to Aecom's estimate. In discussing this alternative last year, the council directed staff to get a second opinion about the cost of the trench from a company that has experience in underground construction.

In considering the contract on Feb. 14, several council members took issue with a provision that empowered Aecom to hire the consultant that would be offering the second opinion on the trench. Elizabeth Alexis, who designed the underpass alternative for the Charleston Road and Meadow Drive crossings, also suggested that this method is unlikely to provide a truly independent opinion.

"I would have some concerns about moving forward with reevaluating things that the current consultant has worked on being led by the current consultant. … It's a very difficult process no matter what, and this would not be a kind of peer review that you would think would lead to any kind of different outcome than what you've already had," said Alexis, who co-founded the rail watchdog group Californians Advocating for Responsible Rail Design.

Several council members shared her concerns. Mayor Pat Burt and Vice Mayor Lydia Kou both suggested that the council is less likely to get a truly independent second opinion if the consultant who conducted the initial analysis is charged with hiring the company that will be reviewing its work.

"What seems to be in the proposal and in the contract is a peer review that would be managed and overseen by the party who did the first item that's being reviewed, which is not really a check and balance in the way that we would hope," Burt said.

Council members Greer Stone and Greg Tanaka both supported sending the item to the council's Rail Committee, which consists of Burt, Kou and Cormack, for further review. Burt noted that the decision on grade separation involves complex and highly technical issues that are ripe for further analysis by the committee.

"If this isn't the kind of work that goes to the Rail Committee, I don't understand the point of having a Rail Committee," Stone said.

Others suggested that failing to approve the contract will delay the process and potentially require the council to proceed with the complex project without outside assistance until the new contract is resolved.

"I'd prefer to see us move forward with some of these without delay," DuBois said.