If it helps, J'onn and Lionel are purely a marriage of convenience. They aren't in love or anything, it's just their cover and J'onn's way of keeping Lionel in check.

I considered bringing the caves into the story, but decided against it - it's cluttered enough as it is. Kyla is just there to lead Kal to his next destination (and the Kawatchee might play a role in the end.)