Helen, you're right to be confused about Alma. On the one hand, she saw something that Ennis cannot explain away and she's heartbroken. On the other hand, things were not resolved completely between Ennis and Alma. It's all a confusing mess, just like everything else in Ennis's life at the moment. When Jack says Ennis will never be happy with her, he's responding to Ennis's not knowing whether he wants to step back into that life.
As for the line about the U.S. Attorney...yeah, that's a hint. But probably no one will ever get it, it's pretty obscure. It will all become clear later. It's just setting up something. God...I feel like such a dork with all these "clues."