1. Was using the same pseudonym in several places.
2. Was advertising the Silk Road. He asked people what do they think about it: "Let me know what you guys think." [1, page 25] - this just suggests that he is connected with it.
3. Used his name (then changed to the same pseudonym he was using in other places) to ask a question about how to connect to Tor using Curl in PHP. He just could ask how to connect to a SOCKS5 server using Curl in PHP whatsoever avoiding mentioning the Tor.
4. Was not using Tor in public WiFi network at cafe.
5. Was giving interviews, long interviews. FBI could correlate his style of writing with what he writes under his own identity.
6. The most grave mistake: he posted his personal Gmail account using his pseudonym (which he was using to advertise the Silk Road) in the Forum asking for a "IT pro in the Bitcoin community" [1, page 26].