I also caught this again yesterday after having seen the first preview in LA (so not sure how much of it was changed over the course of the LA/SF run). I think they really tightened up the flow of the show, especially in transitioning in and out of the musical part, and I'm not sure if some lines just landed better because they're more topical now, or if they were added later. Transitioning it to be about creating a musical rather than a TV show seemed to be an obvious choice, so much so that I wonder why they even bothered with a TV show to begin with (though I do miss the idea of landing in Hollywood Airport, and the even crazier leaps of geography from LA to DC to SF).
The songs seem to mostly be the same, but I think the rally number seemed bigger in my memory (though I believe the Ahmanson also has a bigger stage), and Good Guy with a Gun was reworked, as mentioned, but I really liked how much it paid homage to classic Broadway. I really enjoyed the ending much more this time too, with the transition to all the Asian cast members on stage singing the finale number. And the placement of the orchestra was wonderful, which I enjoyed much more than having them in a pit.
The first act is still a bit rough before they ease into the musical portion, with what seemed to be very heavy-handed declarations about democracy and freedom versus choosing the best person for the job. DHH seems to want to work a little too much of his own experience into it, and not necessarily done very deftly. It reminds me a bit of talking to a child, where they might have some really good ideas but don't know how to communicate them, so they just end up saying the same words over and over as if to say "do you get it yet?", even after we already got the point the first time. The second act opening was much smoother and almost made me wonder if the whole first act intro was really necessary; yes, it does add a bit of weight to the story and ties up the ending nicely, but would it be a better show if it were just removed completely?
I can't quite see it on Broadway anytime soon either, but I do hope they continue to play around with it and see where they can go. If anything, it's so nice to see a cast that is almost fully made up of Asian actors.