I think there is more going on than we know....changing friendships, etc. 2004 was a long time ago. I will be surprised if it is ever released, to be honest.
With regard to censoring the documentary - the "naked" pool scene is such a quick blip and the filming is rough quality...there is not much to see at all. IF it is ever released, I would be more inclined to think that the movie would be heavily edited - removal of a lot of the scenes that John might consider artsy like cuts from musicals, etc. It's been awhile since I saw it, but I can't remember any heavily emotional moments that they wouldn't want shown.