Alrighty, let me take a shot at this....
From what I gathered from Jack's profile, http://bleedman.snafu-comics.com/castJack.php
, it seems Jack came to this time going after Aku. I think what happened in the series kinda happens in reverse here. That is, instead of Aku sending Jack into the future to get away from him, he sends himself into the future with Jack jumping into the portal before it dissappears (not knowing where they are going). When they get to the future, they somehow lose track of eachother.
Given Dexter's comment here, http://www.deviantart.com/view/8395886/
, it looks as though he was the one that found Jack and helped him get settled. With all of his tech, he is bound to find out about some time anomaly (he probably could also forge a birth certificate).
Now this, http://www.deviantart.com/view/11825542/
shows Aku in his "Little Red Hood" outfit. I think that, down the line, Aku finally figures out where Jack has been and goes on the hunt. ((I had thought about a play taking place at school, where Susie plays Hood since she has before. Aku shows up in disguise and looks for Jack with everyone thinking it's just Susie running around...))