Judge Napolitano: Why Prosecute General Petaeus?

Napolitano makes great points here-

One- General David Petraeus had a top security clearance, but Paula Broadwell also had a security clearance. She was in the Army and was approved for promotion to lieutenant colonel in 2013. She was deputy director of Counter-Terrorism Studies at The Fletcher School of Law, she also worked with the FBI Joint Terrorism Task Force. This is not just some girl he met somewhere. They were both military. She had one level of clearance, Petraeus had another.

Second- Napolitano wonders why the DOJ has had this hanging over the head of Gen. Petraeus for 2 years and questions why they have drawn it out for so long. What do they have against him?