Service halted between Brooklyn and Queens so workers could repair damage from Hurricane Sandy.
The G train is so slow that service from replacement shuttle buses is better, many riders said.
Service will be disrupted on the 4, 6, A, C, D, E, F, G, N, R and Q lines.
The A train will not run above 59th Street from 10 p.m. to 5 a.m. Monday through Friday.
The line will close down between the Nassau and Court Sq. stations starting Friday, July 25.
Shuttle buses will replace train service each weekend through the end of May, the MTA said.
The man was hit by the southbound train in the Myrtle-Wyckoff station about 9:30 a.m., the MTA said.
The MTA's FASTRACK program will affect overnight service on the E, M and R lines in Queens until Friday.
The G will run more frequently during the evening rush.
A total of 17 trains lines were set to be re-routed, suspended or delayed this weekend.
The MTA will soon halt weekend 7 trains from Queensboro Plaza to Times Square, until the end of March.
The L train resumed service Thursday, to the delight of Brooklyn riders.
The MTA restored service on the G train Wednesday morning.
MTA closures are coming to Eighth Avenue with service out between Columbus Circle and Brooklyn.
Service on the R line was shut off for a person running on the tracks in lower Manhattan Tuesday night.
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