Do Alec and Jace ever become a couple?

No.

Alec and Jace are Parabati, but they never hook up or become a couple.  Alec believes himself to be in love with Jace in The City of Bones and The City of Ashes, but his affections shift to another.

Jace is never interested in pursuing a romantic relationship with Alec.

Do Clary and Simon ever become a couple?

Clary Fray and Simon start dating in City of Ashes (The Mortal Instruments, book 2).

Simon kisses Clary and then refers to her as his girlfriend. Clary doesn't contradict him and the relationship is begun.