In June 2013, Ulbricht allegedly logged into Silk Road from an Internet Cafe in San Francisco. From there the feds traced his Gmail logs and located his home, 500 feet away, on Hickory Street in San Francisco. They intercepted his mail and found he had allegedly been receiving fake IDs.
Agents visited him on July 26, 2013, and discovered his roommates knew him as "Josh." He declined to answer their questions.
In July 2013, the FBI located the Silk Road server and copied an image of it — all its contents, in other words. They discovered 957,000 registered accounts on the server, of which at least 30% were from the U.S.
Things came to a head in early August, when the FBI arrested a man who was allegedly trading child pornography via a Tor-hosted site called Freedom Hosting.
At that point, "dark web" sites began going offline as users figured out that as much as 50% of the Tor network had been compromised by the feds.
The fact that Ulbricht was still online, and operating Silk Road, through September, is therefore surprising. he had ample warning the feds were after him as far back as June.
In fact, as the indictment against him makes clear, the feds were on to Silk Road back in January 2011. Their investigation discovered him allegedly trying to hire a hitman to take care of an extortionist in March 2013.
The bottom line is that if you were doing anything illegal on Tor or Silk Road for the last three years, you may be screwed.