Anything the NSA does is "secret" so the holes in the FBI arguments, in this scenario, would make sense. An interesting result in this case would be if at any point evidence is not permitted for publication. I wonder if the defence could construct a canary for this possible circumstance.
1: http://daserste.ndr.de/panorama/xkeyscorerules100.txt (note how certain civil liberties are dictated by Geo IP location alone -- that is what I mean by "cowboy mode")
Most likely, the NSA got the information around May, tipped off the FBI and the FBI started working on their "PC" story. Unfortunately, Ross was moving his servers and reconfiguring them during this time, making the PC story a bit more difficult to get.
EDIT: I guess the biggest problem here is that the people responsible for actually perpetrating the crimes (e.g. the police officers lying in court) will most likely not be held responsible.
Also, isn't there a new Silk Road already?
(Citation -- wired article I read at some point; maybe someone else can find it.)
We all are wrong sometimes. Shit happens. :)