The sleeping straphanger was robbed of his passport, ID, social security card and birth certificate.
The A, C and F trains will be shut down between Manhattan and Brooklyn in the future, the MTA said.
Normal service was restored to subway lines that experienced delays Monday morning.
The 43-year-old victim was hit when he tried to walk across the tracks, police said.
Work will affect the 2, 3, 4, 5, 6, 7, A, E, F, G, J, M, Q and two shuttle lines, the MTA said.
Hannah Harris, 20, initially told police she had been carjacked, sources said.
Three women were killed and at least 46 were hurt when the blast leveled two Park Avenue buildings.
A northbound 1 train struck a man in TriBeCa's Franklin Street station, police said.
A man was injured on the southbound platform of the Harlem station, officials said.
Problems at Union Square sparked widespread service disruptions on the 4, 5 and 6 trains Monday.
Schools were open and subways running close to normal for Monday's rush-hour commute.
Police continued their search for a man they said slugged a straphanger on the 7 train.
The high-tech scarf called a Scough is made with "germ-filtering" fabric, its creators say.
Rail problems disrupted many New Yorkers' Thursday commute.
A man attacked another straphanger aboard a 7 train in Queens, the NYPD said.
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