New York's Metropolitan Transportation Authority will conduct a "top to bottom" review of its subway crisis management, said interim chief executive Ronnie Hakim.

The crisis-management initiative will include increased capital spending, Hakim said at Wednesday's monthly board meeting in lower Manhattan.

Breakdowns and delays -- often involving the MTA's aging signaling mechanisms -- have worsened throughout the New York City subway system. Officials have said that aggravation will intensify starting July 8 when Amtrak, which owns Penn Station, begins emergency repair in the station's tunnels, forcing track closures.

"Problems with our aging signal system will not be fixed overnight," Hakim said during an unusually long meeting that featured 25 public speakers. "But how we respond to events can certainly be improved."

At Gov. Andrew Cuomo's urging, the MTA will provide 25% discounts on average to Long Island Rail Road riders inconvenienced by Penn Station delays and reroutings. The discounts are part of an LIRR mitigation plan that will include longer trains, more connections with subway stations and the addition of ferries and buses.

Amtrak chief executive Wick Moorman said the quasi-agency would not reimburse the MTA, said Hakim, acknowledging a letter she received from Moorman on Wednesday. Hakim even hinted at legal action, though several board members advised against such a fight.

Hakim said the MTA is still calculating the cost of the LIRR contingencies. "It's millions of dollars," she said, adding that chief financial officer Robert Foran will reflect it in his financial-plan presentation to the board next month.

The MTA is one of the largest municipal issuers, with nearly $38 billion in debt. On Tuesday it competitively issued $500 million of transportation revenue bond anticipation notes after reducing the size of the sale from $700 million.

Hakim said the MTA will boost capital spending on signaling to $2.1 billion in the 2015 to 2019 capital program. The authority last month increased its five-year capital program request by $2.8 billion, to $32.3 billion. A state review panel must approve the change.

The MTA budgeted $1.3 billion and $1.9 billion in the 2000-to-2009 and 2010-to-2014 capital programs, respectively.

Jamison Dague, director of infrastructure studies at the watchdog Citizens Budget Commission, said the MTA has been mismatching capital spending with state-of-good-repair needs.

"Despite the 10% increase in the size of the plan, the agency still intends to invest less than is required to keep the system in state of good repair and to enable current capacity to be used effectively," Dague said in a commentary.

"The new money and other changes to the capital plan are not wholly aligned with what is needed to get the trains running on time."

Cuomo, meanwhile, is continuing to assert his influence on the MTA board.

On Tuesday he submitted a bill -- just 24 hours before the scheduled end of the legislative session in Albany -- to give the state majority control of the MTA board by adding two Albany-appointed board seats.

The governor essentially controls the MTA board already. He appoints the chief executive and chairman, and gubernatorial appointees represent a board plurality, six of 14 voting positions.

He is expected to make the interim chief executive and chairman positions, which Hakim and Fernando Ferrer now hold, permanent. Thomas Prendergast, who held both positions, resigned from the agency six months ago.

The state Senate this week confirmed three newcomers to fill vacancies on the MTA board and renewed four others.

New members are Carl Weisbrod, an appointee of New York Mayor Bill de Blasio, a senior advisor at HR&A Advisors and former chairman of the New York City Planning Commission; Scott Rechler, a Cuomo appointee, chief executive of RXR Realty, board chairman of think tank Regional Plan Association and former vice chairman of the Port Authority of New York and New Jersey board; and Randy Glucksman, a Metro-North Railroad Commuter Council appointee and vice chairman of the Permanent Citizens Advisory Committee to the MTA. Glucksman will be a nonvoting member.

Weisbrod joins Polly Trottenberg, David Jones and Veronica Vanterpool as city representatives. The Senate reappointed Trottenberg this week along with Ferrer, Andrew Albert and Susan Metzger.

Separately, the MTA hired Cedrick Fulton as president of MTA bridges and Tunnels, effective July 10. He succeeds acting president Tim Mulligan.

Fulton most recently was director for tunnels, bridges and terminals at Port Authority of New York and New Jersey, where he was responsible for managing all six Port Authority bridges and tunnels, plus the Port Authority Bus Terminal and George Washington Bridge bus station.

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