Why didn't they seem fishy to the FBI? If it's so easy to figure out that they were planted, why didn't the FBI figure it out? And if the FBI figured it out, why did they proceed to testify for the prosecution?
What has to be alleged, in order for this scenario to carry any weight, is that CPD and FBI are corrupt and colluding, to frame an innocent man for ??? reason. (IS there a good reason? LE seems okay with the paper delivery person murder being unsolved...they haven't framed HER boyfriend.) Why go to such convoluted lengths...to plant the files, risk calling in the FBI, when they could have put a teaspoon of soil from the site in the soles of Brad's shoes.
What's more likely, to me, is that Brad Cooper is good with computers. He can manipulate files, phones, access computers remotely, cover his tracks at will, and had motive means and opportunity to do all these things.