Bill-
The blinking lights indicate a door error, which is common on the Lionel subway sets. To clear the error press Aux 1 and 0 on the Legacy or Cab1 Remote; the lights will stop blinking and the doors can be opened again.
If the doors still do not open and a buzzing sound in heard, the mechanism is likely jammed or in need of service. Removing the four screws near each truck will allow the shell to be removed. There is no wire harness between the shell and the frame but you will notice a rectangular PC board with contacts sticking up. This board makes electrical contact with a socket on the underside of the shell; when reinstalling the shell ensure the socket is on the same side as the PC board.
Hope this helps!
-John
