http://krebsonsecurity.com/wp-content/uploads/2013/10/Ulbric... / Mirror: http://www.scribd.com/doc/172773407/Ulbricht-Criminal-Compla...
According to the filing, they found him through a combination of posting his personal @gmail.com address on the bitcointalk forum from the same account used to market Silkroad. Further, they found that his LinkedIn account somewhat corroborated the timeline/interest in what Silkroad is. Page 24 for the juicy details of how they identified him.
Also there is a section about murder-for-hire in Canada. Pretty wild stuff.
Update: Also he posted on Stackoverflow asking questions about Tor with his real name, then later changed his name. Supremely conspicuous.