Long Island Rail Road and NJ Transit to Penn Station remained severely strained Friday morning due to an ongoing transit meltdown caused by an East River tunnel fire a day earlier, officials said. The MTA reported the LIRR was running “extremely limited” service into the station during the morning rush, and cancelled all eastbound trains. Officials recommended riders use Grand Central Terminal or Atlantic Terminal as an alternative, and told commuters to expect reroutes, cancellations and delays throughout the day. Midtown Direct service on NJ Transit, which uses the East River tunnels, was still being diverted to Hoboken Terminal, the agency said. Rail tickets are being cross-honored by NJ Transit and private carrier buses as well as the PATH train at Newark Penn Station, Hoboken and 33rd Street. Amtrak said Northeast Corridor service faced delays up to 40 minutes.…