Silk Road was a hidden service so exit nodes were not involved (they would use rendezvous points). If my recollection from American Kingpin is correct, Silk Road was caught because it leaked its IP address in error messages, and Ulbricht posted questions about bitcoin on Stack Overflow using the same name as the bitcointalk post announcing Silk Road. Its clearnet IP was visible for almost the entire lifespan of the site, I believe.