Oh okay, thank you. I was using a totally different tool I found here:
http://code.google.com/p/unyaffs/
I ended up writing a crude script to extract and reconstruct blocks from the image then manually pulling out usr.tgz just to have a look at that, since you graciously uploaded everything else.
My first goal is to figure out a way to easily upload files to the root file system. I'm not confident I could make a custom yaffs2 image that would actually work and I don't want to wear the Kobo prematurely by flashing it repeatedly with tests. Sadly, trying to stick scripts in mfg_test/mfg_test or vform/update_vform on the SD card isn't working. The only other idea I have is to figure out the USB protocol used when updating the firmware. Foxit had a command line tool for updating their eSlick's firmware in Linux here:
http://www.foxitsoftware.com/ebook/gpl.html but, just my luck, all the links are dead and I can't find a mirror.
If I'm able to customize the Kobo a bit (changing the fonts or running 3rd party software) then I ultimately would like to get OpenInkpot running.