I think Jem is going to die too. I love Jem, JESSA FTW! and all that good stuff, but I don't think he's going to make it. I agree with you on Charlotte too, I think with her more or less out of the picture, Henry will have to step up.
I think that either Jem or Will is going to become Brother Jeremiah. He seems to be personally invested into what Jace is doing just for the sake that he, by blood, is a Herondale and the last person to carry the name. Jem is either concerned for the lineage of his now dead Parabatai, or Will is concerned about his name being carried on.
I only disagree with you on Cecily, I think she's going to do something bad. Like get herself killed, fall into an easy trap, or get Tessa/Will/Jem into danger.
I think Will might try to have a relationship with his sister, but she'll be mean and cold to him. Even if he did explain himself, I think she's the kinda character who doesn't forgive easily.