The problem is, if I let the phone just run out of juice, it happens most likely in the middle of the night, so I wont be getting wakeup alarm in the morning
It did, however, charge when using one of the various 'charge21' scripts floating around here on TMO.
it should be possible to run the N900 on AC power alone without battery. Could this be possible in a future version of your bme, pali?