I believe Season 4 is the season that Jax finds out the truth about his father's murder. It may happen mid-season or the end of the season. But it will happen. The timing of the J.T. letters and the source of tension it is creating for Clay, Gemma, and Tara tells me that. That and what Kurt's blog said about the end of this season feeling like a series end but is more like the beginning of the end.
But when Jax finds out the truth about what happened to his father, I don't see him outright killing Clay like Vic didn't outright kill Shane after finding out the truth about his role in Lex's murder. I can see this making Jax decide not to leave SAMCRO and plot Clay's removal from the club while going back to trying to change the club from within but, this time, in more proactive ways.