From what I've skimmed through when I was comparing both (not very thoroughly, I must add!), they used all the second versions, left out the La Bamba snippet (2-01), the band intros (2-10) and The Great Beyond for whatever reason (2-09). That means track order was shuffled, because they incorporated the replayed versions in various places the middle of the setlist.
Most importantly, the bootleg of Unplugged II that we can find all over seems to be taken directly from the soundboard, but the mixing of this final album sounds much, much better. So I got rid of the bootleg.