Well, the packages provided by Sony are for MontaVista Linux, so it's understandable that other distros will require additional patches.
That said, I'm not sure what's the point of rebuilding the kernel at this moment. Is the stock one not working properly or something? The sources for Fsk or UsbUpdater are not public, so you won't be able to reproduce the full firmware (and the kernel wasn't updated in the latest patch anyway).
I'd prefer you've just released the upgrader already, even if just to get the folks from the-ebook.org forums off my back
