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(The following article by Bruce Lambert was published in the New York Times online.)

NEW YORK — The Long Island Rail Road is entering a new and uncertain era. It is merging with Metro-North, riders face proposed fare increases as high as one-third, another shipment of new cars is to be put into service, and now its president is leaving and a successor is being sought.

Kenneth J. Bauer ends his three-year stint as chief of the railroad, the nation’s largest commuter line, on March 3 to become chief financial officer at Railworks Corporation, a private transportation-services company in White Plains.

He is leaving to generally favorable reviews.

“I want to thank you for making a difference,” one passenger, Joan Nemarich, said as Mr. Bauer made a farewell appearance Thursday night at the L.I.R.R. Commuters Council in Manhattan. “You put the emphasis on putting the customers first.”

But the railroad is well known for its glitches and hitches, so there were also complaints about a track fire that shut down Pennsylvania Station for hours on Feb. 14 and the widespread delays after the Washington’s Birthday blizzard.

“This winter has been unbelievably long and arduous,” Mr. Bauer said. But he added that the arrival of the new M-7 electric cars would enable the railroad to better withstand future winters. “The reliability should be a lot better,” he said.

On a typical weekday, the railroad provides 290,000 rides, connecting Nassau and Suffolk with Manhattan, Brooklyn and Queens. The system has about 6,000 workers.

Among his successes, Mr. Bauer pointed to last year’s on-time performance of 94.7 percent, a record. That was achieved despite the railroad’s antiquated fleet and lack of spare cars. Three-fourths of the trains are 33 to 35 years old and are overdue for replacement, but improved maintenance helped keep them running, Mr. Bauer said.

A big headache for the railroad has been correcting the problems in the 134 cars and locomotives of its new diesel-electric bilevel trains. They suffered from structural cracks, air-conditioning that was too cold, recordings that announced the wrong stations and brake hoses that kept separating during last week’s snowstorm.

The bilevel cars were designed and ordered before Mr. Bauer took over, and he was determined to avoid a replay with the M-7 all-electric trains that will replace most of the rest of the fleet.

M-7 prototypes underwent grueling tests, as the railroad hoped to detect flaws and make corrections before going into full production. Four M-7 trains, about 40 cars, are now in service, and the rest of the 678-car fleet will be phased in at the rate of a couple of trains each month for the next few years.

If Mr. Bauer’s testing strategy works, the railroad should be running even better after he is gone, with its fleet modernized from one of the oldest in the nation to one of the newest. Topping Mr. Bauer’s list of unfinished business is the “East Side Access” plan to bring the railroad into Grand Central Terminal, and the extension of the railroad’s track system. “The railroad has not grown since 1898, and look what’s happened to Long Island,” he said.

But getting money for these and other projects is a major hurdle, especially with the stumbling economy, Mr. Bauer said. He hopes the federal government will pay half the costs but conceded, “That’s going to be tough to do.”

As for the merger, he said some functions, like purchasing, might be done better. But the trains of the two systems are not mechanically interchangeable, and the labor contracts at the Long Island are more costly, he said.

Mr. Bauer also wondered whether the sole aim of the merger was to save money, adding, “You don’t want to hurt either railroad.”