Board Thread:TV Show Discussion/@comment-114.71.100.55-20160705071349/@comment-28895263-20171004062918

Other than the name Aegon, there's nothing about the book character Aegon (a.k.a. "Young Griff", Rhaegar and Elia's son) that folds into Jon Snow. Griff and Young Griff were simply dropped from the HBO production.

Your second question is more interesting. I think that Aerys II, Rhaegar, Elia, and their children were all dead before Ned found Lyanna at the Tower of Joy. My reasoning:

Lyanna seemed to know that Rhaegar was dead. Otherwise, why would she have to ask her brother to raise and protect her child? He would be raised at court.

Ned was in King's Landing during, or shortly after, the Lannister army sacked the city. That's when Gregor killed Elia and her children. (Ned found Jamie in the throne room, after Jamie had killed Aerys II.)  Ned would not have left King's Landing until Robert had arrived from the Trident, and was safely installed as King. It's also entirely possible that Ned had no idea of where to find Lyanna. Who told him? Jamie, maybe: he was King's Guard along with Arthur Dayne.

I've read the books, but my knowledge is not encyclopedic. Let's see who chimes in to tell me how wrong I am. :-)