Find out if you really need those Canonical install scripts and make-kpkg. make-kpkg used to be Debian's script for creating distro kernels a long time ago. Debian's kernel team switched to other, more complex scripts a long time ago and make-kpkg has always had some small problems with the latest upstream kernels.
"make deb-pkg" straight out of the upstream kernel works perfectly fine for me on Debian. All I do to install a new kernel from upstream is basically "git pull" and "make -jX deb-pkg" (where X is a suitable number of parallel processes to speed up compilation; make oldconfig is automatically done by deb-pkg) and then sudo dpkg -i the created package.
I only had a problem trying to compile in the radeon driver instead of compiling it as a module, as the initrd creation scripts only install the firmware files required by modules so the driver can not start up correctly.