Same here, I didn't get it at first. But I did enjoy the flashbacks. But when we are shown Detective Hoffman in the morgue, listening to John's tape, founded in his stomach and apparently he poured with wax, as seen in Saw 3 - which he said that his work will continue, it was shown twice.
First time, the morgue scene, was near the beginning of the film, but the second time shown near the end of the film, is when we found out that the tape that John recorded was that he was talking to his next apprentice, Hoffman, about carrying on his work.