Hm...
That's actaully a different processor manual.
I finally found the actual reference manual for the iMX50 series (iMX50RM.pdf).
I couldn't get it to download until I left clicked it, but here's two links to it -- indirect and direct; hopefully others will find this useful for understainding their Kobo's processor...
http://www.freescale.com/webapp/sps/...umentation_Tab
http://cache.freescale.com/files/32b...n&fileExt=.pdf
I also found a program by google search, devregs, which allows the superuser to read the hardware registers on their processor and view the values. It's really handy for debugging device drivers.... or messing with the IO pins on the processor...
just compile devregs.cpp, it's a self contained file, and you too can probe the chip's registers:
https://github.com/boundarydevices/imx-utils
It wasn't written specificially for the iMX50, so it gives an error message on the kobo -- but it still works correctly. There are also two data register definition files in the repository for iMX51 and iMX53 chips which I think have the same addresses as the iMX50.
They unfortunately didn't seem to have the clock control module addresses, so I had to manually enter numbers; but at least those files are handy for looking at other registers.