I think you mean of all three films (or just GF2), because you can probably also adjust the DVD to the chapter order from the novel.

As far as I know, One and Three are chronological.

The young Vito scenes from GF2 are these (if I'm correct):

disc 1: 1, 2, 3, 8, 9, 10, 15, 16
and disc 2: 1, 2, 7

then comes disc 2, scene 13, the surprise party of 1941.
Godfather 1 starts in 1945 and ends in the mid-fifties. The other Two scenes are late fifties and Three is 1979/1980.

I think this is the right order.