Yes he is. In the series finale when Jack picks Jen up and puts him on his shoulder she mentions "the time that CJ knocked me up and left me". I do believe that was something that was sinabi or pretty close to it at least.
no they never sinabi who the father of Jen's baby is all they mention about the baby daddy is when Jack picked her up and she sinabi "hey guys remember when my boy-friend knocked me up and left me to raise a kid on my own" the finale was 5 years into the future therefore the dad could've been any walang tiyak na layunin guy.. If I recall I think C.J either died or moved to a different state I hope this helped..
Whoever sinabi that she mentioned CJ is WRONG. All she sinabi when Jack picked her up was, "remember when my boyfriend knocked me up and left me?" No mention whatsoever of CJ, and knowing what we knew about him, he never would have deserted her.