In a photo made available by the Metropolitan Transportation Authority, trains stand in a flooded Metro-North's Harmon Yard, Wednesday morning, Oct. 31, 2012, on the Hudson Line, in Croton-on-Hudson, New York in the aftermath of superstorm Sandy. (AP Photo/Metropolitan Transportation Authority)
NEW YORK (AP) — Two days after a paralyzing flood, officials announced plans Wednesday to open the undamaged parts of the massive subway and suburban rail systems that are so essential to life in New York City.
The city's transit headaches, though, are far from over.
With some subway tunnels and stations still filled with water and power still off in downtown Manhattan, big gaps will remain in the nation's largest public transit system even after the subways start rolling again Thursday morning.
New York Gov. Andrew Cuomo said there will be no subway service in Manhattan south of 34th Street, an area that includes the city's financial district and many tourist sites.
Commuters who would normally zoom beneath the East River in tunnels that flooded will have to disembark in Brooklyn or Queens and take shuttle buses across a handful of bridges, adding to the enormous stress already being placed on gridlocked Manhattan streets. Around 330 buses were being put into service for the task, the Metropolitan Transportation Authority said.
"We are going to need some patience and some tolerance," Cuomo said.
But the restarting of parts of the system was sure to breathe life back into the city, and allow millions of people to finally get to their jobs, or to school, for the first time since the system shut down Sunday.
To make life a little easier, Cuomo said fares would be waived on the city's subways and buses and suburban trains through Friday.
Limited service resumed Wednesday on two of the city's vital commuter rail systems, Metro-North and the Long Island Rail Road.
Both of those rail systems, which extend many miles into the Connecticut and Long Island suburbs, had been knocked out by power failures, toppled trees, and, in the case of the LIRR, flooding in tunnels beneath the East River.
Grand Central quietly reopened its doors at 2 p.m. with a handful of trains headed to suburban Westchester County.
Banker Mike Brabant took the chance to flee Manhattan, where he had been stranded on a friend's couch since Sunday, when the trains halted in advance of the storm. Pulling a suitcase, he rushed to catch a 2:25 p.m. train for home in Harrison, N.Y.
"There's still no power there, so I have to deal with that," the 51-year old said. "I'll be glad to be back in my own bed. It's been a rough week."
By Thursday morning, 14 of the city's 23 subway lines are expected to be operating, MTA Chairman Joseph Lhota said at a midday press briefing.
Of those, though, only one train, a shuttle between the Port Authority Bus Terminal and Grand Central, was running its full route. Officials said riders should expect delays and factor in up to an hour of extra travel time.
"Our overall goal is to get the system up and running," Lhota said. "Every day, more and more (service) is going to come back."
The MTA was still in the process Wednesday of trying to assess how badly its flooded tunnels and stations had been damaged.
The agency said it had deployed three special trains, each capable of pumping 4,500 gallons of water per minute, to drain the flooded tubes. By the afternoon, three of the seven tunnels that flooded had been pumped out.
That doesn't mean that the subways using those tunnels (the F, 2, 3, 4 and 5 trains) will be returning to service immediately. MTA spokesman Aaron Donovan said all the electrical equipment in the passages, including switches and the third rail, still need to be checked for damage potentially caused by the saltwater and possibly repaired.
But he estimated that restoration of service was probably days, rather than weeks, away.
Restoration of power to the southern part of Manhattan would pave the way for some train lines to extend farther south, and could possibly allow some river crossings. Some subway lines cross the East River on bridges rather than through the flooded tunnels.
Metro-North trains were to run on the Harlem line between Westchester County and Grand Central Terminal. The Long Island Rail Road planned to offer service to Brooklyn's Atlantic Terminal and said some trains would be able to operate into Manhattan.
Vehicle tunnels, including the Brooklyn Battery Tunnel, the Holland Tunnel and the Queens Midtown Tunnel, also took on huge amounts of water. The Brooklyn tunnel alone had an estimated 70 million gallons of water in it Wednesday morning, the MTA said.
That water was being carried out of the tunnel in tanker trucks, the agency said.
The Port Authority's PATH train system, which connects across the Hudson River to New Jersey, was also knocked out by flooding.
Port Authority said it was also still assessing damage and had no timetable for returning service.
Cuomo's announcement came as New York struggles to recover from Monday night's storm.
Bus service has resumed, but the system, which usually serves 2.3 million riders, was plagued Wednesday by overcrowding and traffic delays.
To ease the expected bottleneck, Mayor Michael Bloomberg announced Wednesday that the city's major East River and Harlem River bridges, as well as the Lincoln Tunnel across the Hudson River, would be restricted between 6 a.m. and midnight to vehicles with three or more people. Some traffic lanes would be for buses only. The mayor encouraged people to take a bus rather than drive.
"I know it is an inconvenience for a lot of people, but the bottom line is the streets can only handle so much," Bloomberg said.
Traffic on Interstate 95, crossing into Manhattan on the George Washington Bridge, would be exempt from the occupancy rules, the mayor said.
The Port Authority Bus Terminal, New York's biggest bus hub, also reopened Wednesday. But activity returned slowly, with no Greyhound service and no commuter buses to New Jersey.
Flights slowly got back in the air Wednesday at two major airports, and LaGuardia Airport was scheduled to reopen Thursday. The New York Stock Exchange rang back to life after two days without trading. But large swaths of the city and its northern suburbs — about 1.6 million customers — remain without power.
The subways carry 5.2 million riders daily. The LIRR and Metro-North each has 300,000 daily riders.