I thought the config error was debunked by his attorney. I think the question many people have is if parallel construction was at play and if TOR is compromised.
The FBI argument was 'leaky CAPTCHA'. The defense argument was that the application was hacked. The most likely scenario is an info leak or debug page as Ross was known to live edit/debug the application.
This evidence wasn't tested in court on 4th amendment grounds since the defense didn't demonstrate ownership of the server:
buttcoin.com reported on the leaked ip when it happened, long before it was brought up in court. buttcoin.com was bought by butterfly labs and shut down when they had their assets frozen but dailydot reported on it here: http://www.dailydot.com/news/silk-road-ip-address-leak-drug-...
Silk road was always going down, one way or another.