Another challenge will involve some of the large expansion projects already underway at New Jersey Transit.
Only two others, one each at New Jersey Transit and Metro-North, have four violations.
At New Jersey Transit, 9 percent of the engineers have 54 percent of the infractions in those categories.
Mr. Cooper said he made about $270,000 a year, while the senior vice president for buses at New York City Transit makes $170,000.
Officials at Amtrak and New Jersey Transit said they had no reports of anyone being hit by a train yesterday.
Steve Strauss, a community liaison official at New York City Transit, said his agency would try to minimize the impact of the changes.
Mr. Nagaraja had been the senior vice president for capital program management at New York City Transit, where he was paid $161,000.
Some officials at New York City Transit shook their heads and said it was not possible.
Once a week, on a day off from work, he volunteers at New York City Transit, sweeping stations and giving directions.
Officials at New Jersey Transit said they would not make any immediate changes, either, and would continue with random searches.