@ixtab: Err, you got the wrong file, I did repack usbnet for the PW (that's from a download from the post, to check that I didn't simply upload the wrong package ^^):
Code:
Checking update package update_simple_usbnet_1.1_install.bin
Bundle SP01
Cert number 0
Cert file pubdevkey01.pem
Bundle FD04
Bundle Type OTA V2
Minimum OTA 0
Target OTA 18446744073709551615
Devices 5
Device Kindle 5 Touch Wifi
Device Kindle 5 Touch Wifi+3G
Device Kindle 5 Touch Wifi+3G Europe
Device Kindle PaperWhite Wifi
Device Kindle PaperWhite Wifi+3G
Critical 0
Padding Byte 0 (0x00)
MD5 Hash aea19ffb35240c2e9275135e19fcbf07
Metadata 0
:?
That's confirmed by the name of the bundlefile in your log:
update-simple_usbnet-install.dat
That's what the python packer did (that Yifan tweaked to build his first few K5 packages).
KindleTool always uses
update-filelist.dat 
.