But you should be able to infer location from the gaps. If someone was at station A, then disappears and 2 minutes later is recorded at station be, it should be possible to know they took the train between those two stations.

Yup. There's ample data from metrocards and security cameras to follow his route. The more difficult challenge would be finding everyone he had come in contact with on those trains since data granularity of which cars he took would likely be unspecific.