There are sub-sections of the girls storylines that are completely useless once the book is finished. What's the point of the Black Ajah Hunters storyline? To show how the Black Ajah worked and that there were some people inside the White Tower who were willing to cooperate when the distrust was at its highest. Egwene finds them ... and then they play no part in her storyline after that. The breaking of the Tower is solved due to the Seanchan attack. The Black Ajah is hunted due to Verin telling her how to do it. And later the Black Ajah is defeated when they attack Mesaana in the world of dreams and in various battles in book 14.

The Shaido/Masema storyline took so long to solve (end of book 7 - end of book 11) that it, in the end, became useless. It was neat to know what happened to the Shaido, but Perrin's character development had to be done later by Sanderson in book 13 (finally solving the fear of becoming a wolf, getting skills at Tel'aran rhiod, accepting becoming a ruler), not to mention plot advancements (from book 7 to book 11, Perrin's army doesn't actually grow. The growth comes in book 13, when the matter of the Whitecloacks is solved and a new alliance is made).

I'd think Jain'd become a Hero of the Horn.

He deserves it, although it does make me curious as to why he'd need to tell a Malkieri that "he died clean."

Did it say somewhere that he was a Darkfriend, in an earlier book?

Ishamael used Jain to his uses ("painted him a fool"). How isn't exactly clear, but both Ishy and Jain admit that this happened. Jain is probably ashamed of that, so he tells Mat to tell a Malkieri he died clean. It probably has to do with Isam and how Malkier became part of the blight. Jain caught one of the guys who did it. Maybe he feels guilty of not catching Isam? Or maybe he took part on that process against his will? Who knows? Also, Mat is going to run out of Malkieri men to tell about Jain very soon.

So, I found it interesting, when Jain sacrifices himself for Mat and Thom, he reveals himself and Mat doesn't miss a beat. Mat just acknowledges him as Jain. So did Mat know Noal was Jain the entire time?

Mat just thinks quickly. Remember when he invented a whole backstory of being Thom Grimwell when facing Rahvin in TDR? He did that in a few seconds. Quick thinking, that's all.