I got the feeling that this chapter glossed over a lot, but I'm not exactly certain I want sordid details either. There's a fine line between keeping the story rolling and zipping past potential plot points. Likewise, there's a fine line between fascinating details and bogging the story down with minutiae.
Don't ask me where they are, I'm still looking, too

Atmospherically speaking, I do know that there's too much of a good thing. Too much oxygen on a hot planet and things can spontaneously combust. Heck, too much atmosphere can also be trouble.
Might I suggest tying some of the elements into -ah- more solid compounds? For instance, one could tie down carbon with excess oxygen [not a problem yet] or excess water in extended carbohydrate chains. If you let the nanobugs loose in the air, they could make it precipitate.
Just the idea of making it rain sugar and starch appeals to me, somehow

Call me warped.
...I'm blowed if I can think of a harmless sulphur compound, though...