"The turnpike was jammed."
"This time I'm listening." Closest that man is gonna get to an apology from Jack. LaPaglia plays it well, though.
The flashback to him verbally pounding on Thomas, though . . . okay, you've got a daughter, Jack; Skye was in college, it's not like Thomas was raping some little child; consent is ambiguous and problematic when an authority dynamic is involved, but you are definitely overreacting. (Also, the modern day viewer recalls your affair with Sam.) The line about how he would kill Thomas were he Skye's father and Thomas is lucky Skye's father is dead was really good, though. Even though I suspect my father would not be particularly murderous towards an authority figure I had sex with in college (not that I did, hypothetical scenario here). But then, my father/parents are not representative samples of much of anything.
Also: The guy blacked out 'cause he drank so much. Under all the stress of the constant interrogation, you got him to accept that maybe he really was capable of killing Skye while drunk. Do not give him a timeline of what seems to you a sense-making series of events to written confess "in his own words." This strikes me as beyond the pale. Take it to court, get him to testify that he doesn't remember those 3½ hours and that yes he does believe he was capable of killing Syke Peterson. Do your whole motive etc. song-and-dance and get him convicted. Do not do the equivalent of handing him a confession and asking him to sign.
Wow, Paul was so Jonathan (Danny Strong's character on BtVS).
When Jack was browbeating Paul (the whole "Your wife is out there watching this whole interview" scene) I felt like, "Dude, Jack, don't force a second fake confession. Have you not learned your lesson?" It all turned out fine, but I frequently feel like Jack goes overboard in pressuring suspects to crack.
(Lastly: It makes me sad that it would take so much time -- i.e., more than like 48 hours -- to overturn someone's recanted confession when you've got a new confession, that holds far more water, and new evidence and everything.)