It was not entrapment. There is mention of undercover purchases and a controlled delivery by law enforcement, but these are not entrapment. Most of the evidence came from his own laptop.

Didn't Ulbricht actually run the Silk Road? Did someone from the FBI persuade Ulbricht to do it?

By accepting the pardon the accused concedes to guilt in the crime.

Yes the FBI had root or admin access to the Silk Road system and could have very easily changed or otherwise affected logs/record IDs that the technical case rested on. Two of the FBI agents on the case were later punished for corruption on the case.