The Metropolitan Transportation Authority said Monday that of all the damage it's still fixing from Sandy, restoring the complete run of the R train is its priority. Other trains, including the J and the Z, will take some time to restore as well. NY1's Tina Redwine has the story.

Ever since Sandy hit, the R train has been in two sections-- one from Queens to Herald Square in Manhattan, the other in Brooklyn from Bay Ridge to Jay Street.

To get across the East River, many riders in Brooklyn are switching to the already overcrowded 4 and 5.

"The sooner we can get service restored in some kind of incremental fashion on the R, the better off we'll be," said Thomas Prendergast, president of MTA New York City Transit.

The MTA says in a few days the R will reopen from Herald Square to Rector Street.

At roughly the same time, the J and Z trains will again make stops at Broad and Fulton. But the authority says it could still take two weeks to resume R service through the tunnel between Brooklyn and Manhattan because the tunnel carrying the R saw the worst flooding.

"Over one hundred relays were damaged by salt water," Prendergast said of the tunnel. "So we either have to replace them or clean them out and make them dry."

But even then don't count on trains stopping anytime soon at the first stop in Manhattan --Whitehall station. Prendergast said just assessing the damage in an arduous process.

"The escalator at the south end, we don't know the damage," he said. "It's a long vertical climb upstairs."

Prendergast said it will be months before riders can use the 1 train stop at South Ferry station or hop on the A train to the Rockaways.

The MTA said once full service is restored it will examine how it can best use its limited funds to protect the system from future flooding.

"If we could get two or three more trains that were pump trains then it would be an investment we could make because we have the rolling stock," Prendergast said.

But the MTA said expensive structural changes to protect the subway will have to be funded by the federal government.

Washington will need to add that to the billions of dollars the MTA said it already needs to just fix the system.