Well, I don't think anyone will have much of a clue how to fix it without doing a full restore, since any number of things could have been corrupted when you ran the battery totally dead. Asus won't do anything but the F9 restore, without caring about your personal data.
To recover the files you have on there, you can try booting a Linux distribution meant for recovery. Use the directions for installing it onto a USB thumb drive, it will work fine on the SD card. To boot from the SD card, hit 'Esc' when first booting, it will bring up a menu that will allow you to boot from the card.
After you have everything backed up, run the F9 restore, which will bring it back to the condition it was in out of the box.
For the future, don't run the battery totally dead again, it is not only bad for your data, it is bad for your battery.
Last edited by elliott678; 01-11-2009 at 12:36 AM.