Let me try out an interpretation of the toilet scene. I'm not certain of this interpretation, not by a long shot, and I'm curious if this makes sense to anyone.
I wonder if the key isn't in the last few sentences:
I seen they'd cut me different like you'd crop a ear or scorch a brand. No way to get it right with him after that.
I know Jack's talking about being circumsized. But, well, is there more to it than that? I mean, here's a gay man saying that, somewhere far back in his childhood, he recognized that he was different from his father, in some way related to their sex organs. And then he says that there's "no way to get it right with him after that."
So... my take is that Jack knew he was attracted to men, sometime far back in his childhood. And although he probably never came out to his parents, he felt at some gut level that his sexual orientation, this fundamental difference between him and his father, was the root of their conflicts.
And what's odd, and incredibly sad to me, is that Jack seems to regret not being able to "get it right with him." As if Jack thinks it's his fault.
And there seems to be some self-loathing in the imagery ("scorch a brand"? "crop an ear"?), too, which also strikes me as incredibly sad, especially in the character who seems more comfortable with himself.
(I've also wondered if Jack's restlessness and desire to leave home was the result of knowing that he was attracted to men, and feeling like he couldn't fit in at home because of it.)
(I still don't think that scene is the best way to convey that information, though. The implied child abuse just overwhelms everything else for me. Maybe it's particularly bad for me, though; I've got a three-year-old son who has recently been potty trained.)