There's another tiny but critical missing part:
In the DVD "extras" disc, we see that great scene in which Gardiner Shaw asks for permission to marry Sonny's daughter Francesca. On the DVD, it ends with Michael joking Gardiner about taking a course in business. In the TV chronological version, there's about a ten-second additional piece in which Michael then turns to a big, hulking young man in a plaid sportcoat and says, "How are you, Santino?" "Fine, Uncle Mike," the young man replies. We're seeing Sonny's second son in a (brief) speaking role. We saw his oldest son, Frank, in a speaking role in GF, when he presented Vito with a get-well card when Vito returned from the hospital.
I'm not sure of this, but I think maybe the DVD extras disc doesn't include a scene at that party in which Anthony starts to head for the boathouse while Michael's having his meetings, and Kay, looking very worried, grabs him and stops him. This is a nice setup for the later scene when Michael and Kay are dancing, and she upbraids him about how he pledged to be legit in five years--and "that was seven years ago."