Thanks for all the replies.

So just a follow up with more details:

 1. I used the kernel-package (make-kpkg).
 2. Built the kernel from linux-2.6 git tree. I needed kernel version
    3.6 since it fixed a bug that I really needed fixed.
    - Can I build kernel 3.6 by customizing debian:src kernel package?
 3. I did built with --initrd but as I mentioned in the previous mail,
    initramfs tools are downloaded and installed after linux-image so in
    order to get it to work I had to add a hook that did the following:

    #+BEGIN_SRC sh
    set -e
    echo "linux-image-3.6.0-0-amd64 \
    linux-image-3.6.0-0-amd64/preinst/overwriting-modules-3.6.0-0-amd64 \
    boolean false" | debconf-set-selections
    apt-get install --reinstall --yes --force-yes linux-image-3.6.0.0-amd64
    #+END_SRC

    The debconf-set-selections was needed so that I did not get a prompt.

 4. And had to add the following option to lb config: --apt-options
    "--yes --force-yes".


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