Andrea Held Leone is Mike's late mother, and Ralph R. Dominici Sr. is Charlie's father.
According to Mike, it was about a friend of theirs who was busted for stealing and the experience he gleaned from it.
Ytsejam is Majesty (DT's original band name) written backwards. It doesn't have any actual "meaning".
John doesn't comment on it often, but Mike Portnoy opened up in an interview about why it was written and what he thinks it's about. In the interview, Portnoy was very careful to remind the reader that he could be all wrong, but that it was not likely.
Petrucci wrote it as a sort of Twilight Zone story about war, in which the main character witnesses all these atrocities and sees the names of the dead on a wall. He then realizes it had been him the whole time causing the atrocities... then he sees his own name on the wall.
While the band admits Afterlife has christian overtones, it is not a religious tune in the same spirit as the music of King's X or Parallax. In fact when the band used to play Afterlife live with Chris Collins, the lyrics were completely different.