I am also doing a similar research, not very seriously yet. Right now I'm dumping the images of the mounted partitions, using commands like this:
dd if=/dev/block/mmcblk0p5 of=/extsd/data.img
In principle one can recover the partitions, by interchanging if and of. Of course, this will only work if the system is more-or less working (either WIFi + sshd, as I'm doing now, or adb over USB). I'll also dump the non-mounted partitions.
There must be a way (a special key combination?) which would initiate the system recovery, from mmcblk0p2 on a hardware level (even with a bricked unit). Does anyone know how to do that? I heard Kobo's customer support can be very helpful in this matters - may be I should send them an email. I tried many different combinations (simultaneously pressing two or more of power, volume up/down, back, menu, home buttons) - either from a powered on, or powered off positions, to no avail.