What clues? My bad on "Coddington". I just finished ADWD a few days ago, and probably need to read them again to catch some of this stuff.
Most of them stem from Ned's time in the black cells when he is having his flashbacks to the tower of joy.
Why were three members of the Kingsguard there if not to protect the heir?
Lyanna was said to die in her bed of blood, Martin has used the term bloody bed to signify child birth multiple times throughout the series.
Lyanna was found clutching blue roses when she died, the same type of rose Rhaegar gave her when he crowned her at harrenhall.
She made ned "Promise her". We believe that promise was to keep her son safe from Robert.
Ned feels immense guilt towards Jon at the end and wishes to have one more conversation with him, however he doesn't have these feelings towards any of his other children.
I thought Rhaegar only had 2 kids (a boy and a girl)?
The only two the realm knows about and Robert had them both killed. Which is why keeping Jon's identity a secret would be of the upmost importance to Ned.
This post was edited on 8/14 at 7:16 pm