Without something to base the original shows on (all I had was my memories) I cannot comment with complete authority on any missing material. Judge makes a couple of comments in the bonus material that might help.
He says that there is some random violence and a scene of paint thinner sniffing added back into the episodes. He also pulls the old REN AND STIMPY argument saying that Paramount cut many of the shows for syndication/censorship issues way back when and now no longer "owns" the episodes in their original form. Since he does not own the show, this is the version of the series he is 'stuck' putting out.
I will say, as much as I enjoy B&B, the lack of vidoes - and now this information - makes me suspicious about sets 2 and 3.