They didn't get him via TOR. If you start reading on page 26, it states that Jeremy hammond revealed personal info to the confidential witness (CW-1). It was this personal info he shared that was used to identify Hammond as the suspect.
It's interesting because the FBI was in a perfect position to perform the most well-known attack on Tor: a correlation / timing attack. "If your adversary can watch both ends of the connection, you lose." They could watch his end and probably knew where the chat server was located. If it was located in the US, it would have been pretty straightforward to send an agent / install a device at the data center and watch t…
Also, the surveillance you disclose in explanation of finding him, and the surveillance you do for the sake of having some surveillance to disclose.