There are small differences in audio and performance. For example, I've been listening to Sacramento and Portland and am now almost completing Portland download so I can start editing. I've done some of my own audio mixing to try and improve the audio a tad, but since it's just on stereo file, the differences in instrument volume can't really be affected all that much, for instance. In Sacramento, both the lead guitar and bass seem to be too low. On the other hand, in Portland, I feel Trent's lead vox are just a tad too low. And in both of them the background vox should be higher at some songs IMO. And yeah, when I say these things it doesn't automatically mean every song is like that, but in some the "problems" are attenuated.
Then there's performance... and that's a whole different ordeal. Some of the guitar work I like better in Portland, some in Sacramento. Some parts of of some songs with Trent singing I like the improvised notes in Sacramento better. Oh, and Josh Freese's drumming at the end of Survivalism is much nicer in Sacramento with those nice tom fills.
I'm still wrestling with the question of if I should try to replace for the Portland picture edits the songs in which I like the Sacramento performance better.. or just go with the original songs of that concert. Needless to say, there also might be some sync issues since they're not (luckily) machines. Well, except maybe for Freese, but he's a machine in a good way.
