As for 1 I believe they use the old South Ferry loop.. the water has been pumped out from the loop and that track is now usable
The track is not the only thing that makes the station work.
Both the South Ferry Loop and Island station have been flooded due to their low elevation at the tip of the island. Neither are in operable service to serve trains or passengers, regardless if only the tracks were flooded, and are undergoing repairs at the moment. Check the MTA Photos page on Flickr to keep track of the damage, and check to see if MTA plans to reroute trains to the loop anytime soon while they continue repairs on the Island station. It's a shame that all that money used to build the new South Ferry got put to test, but it's a lot better than it not being salvageable, at all.
Rector street is not a terminal station, so there are no layups to service terminal trains, nor are there any free transfers between northbound and southbound trains. Terminating a station ahead of the flood is not a good practice, either. And due to its vicinity to the Cortlandt Shell (and around it, the ongoing construction at the World Trade Center) trains cannot idle in the tunnel while construction is going on around it. Chambers was chosen so that the 2 train goes local leaving the 1 to utilize the center tracks from 96th downward, and then reroute right before Chambers.
BStyles