1. Use apt-get source to download the Ubuntu version of the kernel

apt-get source linux-image-$(uname -r)

gives a folder that contains, for example:

linux-3.2.0                linux_3.2.0-26.41.dsc

linux_3.2.0-26.41.diff.gz  linux_3.2.0.orig.tar.gz

The bolded diff includes all the Ubuntu/Debian customizations.

2. To build a stock kernel with your own .config, use the "old-fashioned" Debian make-kpkg method

This is the alternate old-fashioned way described in the wiki:

sudo apt-get install kernel-package

If you are compiling a kernel for the first time:

sudo apt-get build-dep linux-image-$(uname -r)

Then cd into the source directory (here, linux-3.2.0), and either run make oldconfig to create .config file with your running kernel's configuration, or copy a third-part .config to this directory.

Depending on whether you want a text or graphical config, install:

(Text)

sudo apt-get install libncurses5 libncurses5-dev

(Graphical)

sudo apt-get install qt3-dev-tools libqt3-mt-dev

And then run:

(Text)

make menuconfig

(Graphical)

make xconfig

When done, just run:

fakeroot make-kpkg -j N --initrd --append-to-version=my-very-own-kernel kernel-image kernel-headers

where N is how many jobs to run in parallel (usually the number of CPUs you have), and my-very-own-kernel is a custom string to identify this build.

When done, the kernel image and header files will be ready as debs in the parent directory; you can install them with sudo dpkg -i, which will also take care of adding GRUB entries, etc.