Almost all of the city’s subway system is back in operation after Hurricane Sandy, but the parts that still aren’t working are very broken. The Montague Tunnel, through which the R train passes between Brooklyn and Manhattan, saw the worst flooding of any, with water reaching all the way into Brooklyn Heights, within 500 feet of Court Street station. “That’s a long distance and the water was floor to ceiling,” MTA chairman Joe Lhota told the New York Daily News. The tunnel won’t be back up and working for “several weeks,” meaning no R train service between Brooklyn and Manhattan for that time. Meanwhile, the North Channel Bridge, which connects the Rockaways to Howard Beach, won’t be able to handle train traffic for another week or so, as workers scramble to repair severe track damage there. By now riders on those lines have probably mastered the alternative routes, which for Rockaway residents trying to get to Manhattan means a shuttle bus to Howard Beach. At least the buses have heat.