Tyler -
It's true that bacteria aren't a major issue for modern humans, but modern humans happen to be among the most hostile places imaginable for bacteria. Lacking complex adaptions to help, it makes more sense for a bacteria to survive the rigors of space than to survive on our skin; of course, they do have those complex adaptions, and those adaptions do cost a lot of energy. They're just superior to the alternative, eg. death.
Part of the reason for making replicating nanotechnology fragile, as I see it, is that this way we'll be much less likely to see the sort of runaway weapons race that has led to an environment where replicators must devote most of their resources simply to avoid being killed by other replicators. It's a fresh start. Let's make the most of it.
Given that the number of parts in the story has been explicitly stated all along, I doubt it'd change in length.
No, you've got to suggest someone else to stun, I'm pretty sure.
One thing I'm wondering about the superhappys. They're so eager to cooperate, even to the point of changing their own utility function; what would happen if they kept running into one alien race after another, all of which would alter it in the same direction?
I can't figure out a better solution than what they've proposed. I wouldn't particularily want to eat nonsentient babies - it seems so pointless, by all three pre-existing utility functions - but so is art, by the happyhappyhappys' function.
Eliezer, if your point is to emotionally drive the point that utility functions are basically arbitrary, you've succeeded.