I am sorry for your loss. ):
2 weeks isn't very long for not pooping (for ball pythons). Chances are he didn't need the soak, and even if he did, it probably didn't need to be more than 10 minutes. 2 inches is probably too much unless he was huuge. Usually you only use enough water to go halfway up the sides of the BP.
I have heard that ball pythons can hold their breath for a pretty long time.
Did you poke air holes in the container?