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.
It was entrapment because federal agents posing as crime bosses were threatening Ross that if he didn't hire the hitman there would be serious consequences. He was manipulated and forced into the position he was in.
This is not necessarily true. In Burdick v. United States it does say "an imputation of guilt and acceptance of a confession of it" but there is debate about whether it is binding of not.
Apparently, there is something in Lorance v. Commandant, U.S. Disciplinary Barracks that indicates that accepting a pardon does not imply guilt, but I am not very knowledge on that.
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.