Did Hannibal Kill Miggs?

He was talked into swallowing his tongue by Dr Lecter after Miggs threw semen at her. Lecter found this act to be discourteous and "unspeakably ugly" and decided to kill Miggs. Miggs was found dead the next day, after Lecter manipulated him into choking on his own tongue.

What did Miggs throw at Clarice?

While Clarice was talking with Lecter, Miggs started masturbating and when Clarice passed his cell again, Miggs threw his semen in her face.

How did Clarice's father die?

She tells Lecter that she was raised in a small town in West Virginia with her father, a police officer. When she was about 10 years old, her father was shot when responding to a robbery; he died a month after the incident.