Despite OP's original agro, there's actually nothing that they've mentioned that I (and many others) haven't also experienced.

RootFS full? yep.

Laggy phone? yep

Mysterious battery drop? yep

Losing repos for no known reason (then magically re-appearing...) yep

Whilst I can't talk for the hammering that emulators might give the battery, I can certainly say that I've had most of these problems over the year or so that I've owned my N900.

the shite phone lock, unable to answer calls, proximity sensor fail problem occured for me (for the first time in a while) last week, and guess what? My FIRST thought was "This sucks balls!"

Reflashing fix my problems? Yep. Lucky me for being at home with my laptop and USB cable.....