makaveli,
From the description of the issue with going back to LiveCD chroot, and grub being unable to automount /boot this tells me you're not mounting your partitions. Going back to the LiveCD, you have to duplicate the process of mounting your / partition on /mnt/gentoo and then mounting any additional partitions under /mnt/gentoo/boot or whatever. Also when doing the grub install, assuming you're in the LiveCD chroot things have to be mounted before chrooting.
Also once you get things working, keep in mind that gentoo does not normally mount /boot. You have to mount boot before doing anything with grub or copying bzImage or System.map.
I'm doing everything on single IDE drives, so I can't help with the details there but I'd make sure you have usb mass storage & friends compiled in for a USB drive.
The gentoo forums would probably be more helpful, even just to search for a similar setup. But whatever
Good Luck!
--glenn