New kernel

Hi, I'm trying to install a new kernel for PelicanHPC 1.9. I need to include perfctr patch.
I have followed these tips: http://www.complang.tuwien.ac.at/anton/build-debian-kernel.html
I added patches for squashfs and aufs (as modules) too.
I work in a chroot environment using uncompressed filesystem.squash as /
I installed my new kernel .deb file, I added new vmlinuz and initrd.img to pelican/live/ folder.
I edited pelican/isolinux/menu.cfg as well.

When I boot this modded PelicanHPC I got this error:

mount aufs on /root failed with option noatime,dirs=/cow=rw://filesystem.squashfs=rr

If I boot with PelicanHPC original kernel, everything is fine.
I don't know if I'm doing it the right way. Any feedback is welcome.
Thanks,
hamen